Variant report

Variant	rs1008710
Chromosome Location	chr15:42142392-42142393
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42139809..42142475-chr15:42153474..42155142,2	MCF-7	breast:
2	chr15:42136531..42140635-chr15:42140718..42144467,4	MCF-7	breast:
3	chr15:42127281..42132563-chr15:42140689..42145219,5	K562	blood:
4	chr15:42133144..42136683-chr15:42139373..42142777,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EHD4-1	chr15:42142067-42142770	NONHSAT041973

Variant related genes	Relation type
ENSG00000168970	Chromatin interaction
ENSG00000243789	Chromatin interaction
ENSG00000243708	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1061354	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10775123	1.00[CEU][hapmap]
rs1081022	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[EUR][1000 genomes]
rs11070347	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs11070350	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1197666	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1197670	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1197704	0.85[CEU][hapmap]
rs1197772	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs12148330	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs12441249	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs12915325	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs12916992	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs1648827	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1648828	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1648829	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1648830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1648831	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1648832	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1648833	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1648834	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1648835	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1672464	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1672465	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1672466	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16972089	0.93[CEU][hapmap];0.84[CHB][hapmap]
rs16972136	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1867417	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1899820	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1899821	1.00[CEU][hapmap]
rs1918314	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2178004	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2577947	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2577950	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2577951	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2577954	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2577959	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2605570	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs2695163	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2695164	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2695169	0.93[CEU][hapmap]
rs2925337	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs3784282	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4078788	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4465584	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs4923908	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs4924568	1.00[CEU][hapmap]
rs4924572	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs57498313	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7165230	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7169496	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs7177911	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs7178205	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs8034261	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs8038783	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs8039440	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs890508	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv904115	chr15:42076387-42171483	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv904116	chr15:42076387-42229852	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
5	nsv1038393	chr15:42083574-42188035	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	esv1827003	chr15:42087505-42199076	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	esv1816120	chr15:42093384-42171578	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
8	nsv1041645	chr15:42095168-42186482	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1051200	chr15:42095168-42188035	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
10	nsv517631	chr15:42096926-42187492	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1051733	chr15:42098896-42186482	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
12	nsv1036153	chr15:42098896-42188035	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
13	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
14	nsv1048606	chr15:42101694-42192760	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
15	nsv904117	chr15:42103822-42184794	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
16	nsv904118	chr15:42103822-42207905	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
17	nsv904119	chr15:42109975-42142912	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
18	nsv904120	chr15:42109975-42153085	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
19	nsv904121	chr15:42109975-42162957	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
20	nsv904122	chr15:42109975-42166475	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
21	nsv904123	chr15:42109975-42171483	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
22	nsv904124	chr15:42109975-42207905	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
23	nsv9244	chr15:42110712-42208805	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
24	nsv904125	chr15:42119900-42210393	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
25	nsv1050892	chr15:42128855-42186482	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
26	nsv904126	chr15:42132896-42171483	Enhancers Strong transcription Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
27	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1008710	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42121000-42147400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:42121400-42147600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:42121400-42147600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:42122000-42142400	Strong transcription	Fetal Stomach	stomach
5	chr15:42122000-42142600	Strong transcription	Fetal Intestine Small	intestine
6	chr15:42122200-42145400	Weak transcription	HepG2	liver
7	chr15:42122400-42142600	Weak transcription	Fetal Brain Male	brain
8	chr15:42124200-42142400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr15:42125600-42142400	Weak transcription	Dnd41	blood
10	chr15:42126200-42152400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:42127000-42143600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:42131000-42162800	Weak transcription	HSMM	muscle
13	chr15:42131800-42142600	Weak transcription	Psoas Muscle	Psoas
14	chr15:42132200-42143400	Strong transcription	Fetal Muscle Leg	muscle
15	chr15:42132600-42142400	Strong transcription	Right Ventricle	heart
16	chr15:42132800-42142600	Strong transcription	Fetal Brain Female	brain
17	chr15:42133000-42142400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr15:42136400-42146800	Weak transcription	Fetal Kidney	kidney
19	chr15:42138200-42173400	Weak transcription	Right Atrium	heart
20	chr15:42138800-42142400	Weak transcription	Osteobl	bone
21	chr15:42139200-42142800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:42139200-42144000	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:42139800-42143000	Strong transcription	HUVEC	blood vessel
24	chr15:42140200-42142400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:42140400-42147800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:42140600-42142400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:42140600-42142400	Weak transcription	Brain Substantia Nigra	brain
28	chr15:42140600-42143200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:42140600-42143200	Weak transcription	Primary B cells from cord blood	blood
30	chr15:42140800-42142600	Weak transcription	Stomach Mucosa	stomach
31	chr15:42140800-42143200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr15:42140800-42144600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr15:42141000-42142600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:42141000-42142600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:42141000-42142600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr15:42141000-42143200	Enhancers	HMEC	breast
37	chr15:42141000-42143600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr15:42141000-42144000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr15:42141000-42144400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr15:42141000-42146400	Enhancers	Fetal Lung	lung
41	chr15:42141000-42147200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:42141000-42147400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:42141000-42147600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr15:42141000-42149400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:42141000-42152200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr15:42141000-42154600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:42141200-42142400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:42141200-42142400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:42141200-42142800	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr15:42141200-42142800	Weak transcription	Rectal Mucosa Donor 29	rectum

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