Variant report

Variant	rs1197670
Chromosome Location	chr15:42138321-42138322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42136531..42140635-chr15:42140718..42144467,4	MCF-7	breast:
2	chr15:42119559..42121524-chr15:42137744..42139506,3	K562	blood:
3	chr15:42128850..42133555-chr15:42135364..42139036,5	K562	blood:

Variant related genes	Relation type
ENSG00000137877	Chromatin interaction
ENSG00000250379	Chromatin interaction
ENSG00000243789	Chromatin interaction
ENSG00000243708	Chromatin interaction
ENSG00000168970	Chromatin interaction
ENSG00000200293	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1008710	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1061354	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1081022	0.86[EUR][1000 genomes]
rs11070350	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634840	0.81[EUR][1000 genomes]
rs11855017	0.84[ASN][1000 genomes]
rs1197666	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1197768	0.84[ASN][1000 genomes]
rs1197769	0.84[ASN][1000 genomes]
rs1197772	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12441249	0.81[EUR][1000 genomes]
rs1648827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1648828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1648829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1648830	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1648831	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1648832	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1648833	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1648834	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1648835	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1672464	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1672465	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1672466	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16972089	0.82[EUR][1000 genomes]
rs16972136	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1880937	0.81[ASN][1000 genomes]
rs1880938	0.84[ASN][1000 genomes]
rs1918314	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2250964	0.81[ASN][1000 genomes]
rs2577947	0.81[ASN][1000 genomes]
rs2577950	0.81[ASN][1000 genomes]
rs2577951	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577952	0.84[EUR][1000 genomes]
rs2577953	0.81[ASN][1000 genomes]
rs2577954	0.81[ASN][1000 genomes]
rs2577955	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577958	0.84[ASN][1000 genomes]
rs2577959	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2605570	0.86[ASN][1000 genomes]
rs2695162	0.81[ASN][1000 genomes]
rs2695163	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2695164	0.81[ASN][1000 genomes]
rs2695166	0.84[ASN][1000 genomes]
rs2695169	0.81[ASN][1000 genomes]
rs2918051	0.81[ASN][1000 genomes]
rs2925337	0.87[ASN][1000 genomes]
rs3743028	0.83[ASN][1000 genomes]
rs3784282	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4078788	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4371125	0.83[EUR][1000 genomes]
rs57498313	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7164209	0.81[EUR][1000 genomes]
rs7165230	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8028886	0.83[EUR][1000 genomes]
rs8038783	0.83[EUR][1000 genomes]
rs8039440	0.83[EUR][1000 genomes]
rs890508	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1197670	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 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	chr15:42121400-42138400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:42121400-42138400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:42121400-42138400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:42121400-42138400	Weak transcription	Primary B cells from cord blood	blood
6	chr15:42121400-42147600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr15:42121400-42147600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:42121600-42138600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:42121600-42141400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:42121600-42141800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr15:42121800-42140400	Weak transcription	Hela-S3	cervix
12	chr15:42122000-42142400	Strong transcription	Fetal Stomach	stomach
13	chr15:42122000-42142600	Strong transcription	Fetal Intestine Small	intestine
14	chr15:42122200-42145400	Weak transcription	HepG2	liver
15	chr15:42122400-42142600	Weak transcription	Fetal Brain Male	brain
16	chr15:42124200-42142400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:42125400-42142200	Weak transcription	GM12878-XiMat	blood
18	chr15:42125600-42142400	Weak transcription	Dnd41	blood
19	chr15:42126200-42142000	Strong transcription	Primary T cells from cord blood	blood
20	chr15:42126200-42152400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr15:42126600-42140400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr15:42126800-42141600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr15:42127000-42141600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr15:42127000-42143600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:42128200-42141600	Strong transcription	Fetal Intestine Large	intestine
26	chr15:42128600-42138800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:42128600-42139800	Weak transcription	HUVEC	blood vessel
28	chr15:42128600-42141200	Strong transcription	Ovary	ovary
29	chr15:42130400-42138800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr15:42131000-42140400	Weak transcription	HMEC	breast
31	chr15:42131000-42162800	Weak transcription	HSMM	muscle
32	chr15:42131200-42141000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:42131800-42138600	Weak transcription	Stomach Mucosa	stomach
34	chr15:42131800-42141000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr15:42131800-42141400	Strong transcription	Brain Cingulate Gyrus	brain
36	chr15:42131800-42142600	Weak transcription	Psoas Muscle	Psoas
37	chr15:42132000-42141200	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:42132000-42141800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:42132200-42141400	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr15:42132200-42141600	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr15:42132200-42141600	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr15:42132200-42141800	Strong transcription	Brain Germinal Matrix	brain
43	chr15:42132200-42143400	Strong transcription	Fetal Muscle Leg	muscle
44	chr15:42132400-42141400	Strong transcription	Brain Angular Gyrus	brain
45	chr15:42132400-42141600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:42132400-42141600	Strong transcription	Pancreas	Pancrea
47	chr15:42132400-42141800	Strong transcription	Thymus	Thymus
48	chr15:42132600-42141000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:42132600-42141200	Strong transcription	Lung	lung
50	chr15:42132600-42141400	Strong transcription	Skeletal Muscle Female	skeletal muscle

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