Variant report

Variant	rs1197704
Chromosome Location	chr15:42083094-42083095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42068588..42069246-chr15:42082869..42083482,2	K562	blood:
2	chr15:42049130..42051110-chr15:42082054..42084370,2	MCF-7	breast:
3	chr15:42081345..42083475-chr15:42119441..42122025,2	K562	blood:
4	chr15:41952932..41955703-chr15:42081114..42083481,2	K562	blood:

Variant related genes	Relation type
ENSG00000250379	Chromatin interaction
ENSG00000243789	Chromatin interaction
ENSG00000168970	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1008710	0.85[CEU][hapmap]
rs10775122	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs10775123	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs1081022	0.85[CEU][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs11070347	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs11855017	0.85[ASN][1000 genomes]
rs11857301	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1197666	0.83[CEU][hapmap]
rs1197768	0.83[ASN][1000 genomes]
rs1197769	0.83[ASN][1000 genomes]
rs1197772	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs12148330	0.85[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap]
rs12441249	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs12915325	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap]
rs12916992	0.90[CHB][hapmap]
rs1648830	0.85[CEU][hapmap]
rs1648833	0.83[CEU][hapmap]
rs1648834	0.83[CEU][hapmap]
rs1648835	0.85[CEU][hapmap]
rs1672465	0.91[CEU][hapmap]
rs1672466	0.85[CEU][hapmap]
rs16972089	0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs16972136	0.85[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs1867417	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs1880938	0.83[ASN][1000 genomes]
rs1899819	0.84[CEU][hapmap];0.90[CHB][hapmap];0.86[YRI][hapmap]
rs1899820	0.82[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap]
rs1899821	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs1918314	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs2178004	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs2577947	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs2577950	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs2577951	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs2577952	0.99[ASN][1000 genomes]
rs2577954	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs2577958	0.83[ASN][1000 genomes]
rs2577959	0.85[CEU][hapmap];0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs2605569	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2605570	0.90[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2695163	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap]
rs2695164	0.85[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs2695165	0.87[ASN][1000 genomes]
rs2695166	0.83[ASN][1000 genomes]
rs2925337	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4244585	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs4371125	0.80[CHB][hapmap]
rs4465584	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs4923908	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs4924568	0.85[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs4924572	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap]
rs7169496	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs7177911	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs7178205	0.85[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap]
rs8034261	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs8038783	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap]
rs8039440	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1036086	chr15:42004962-42091451	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers 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 target site	15 gene(s)	inside rSNPs	diseases
3	nsv1054671	chr15:42016097-42098896	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv2757597	chr15:42047173-42122617	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	esv2760027	chr15:42047173-42122617	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv904113	chr15:42050390-42118971	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription 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 target site	19 gene(s)	inside rSNPs	diseases
7	nsv904114	chr15:42050390-42119900	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1197704	MGA	Cis_1M	lymphoblastoid	RTeQTL
rs1197704	MAPKBP1	cis	cerebellum	SCAN
rs1197704	SNAP23	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42070200-42109800	Weak transcription	Fetal Brain Male	brain
2	chr15:42071000-42092800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:42071200-42092000	Weak transcription	Brain Germinal Matrix	brain
4	chr15:42079000-42085200	Enhancers	Fetal Intestine Large	intestine
5	chr15:42079200-42084000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:42079200-42090000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:42079800-42084000	Enhancers	Primary B cells from peripheral blood	blood
8	chr15:42079800-42089000	Enhancers	HMEC	breast
9	chr15:42080400-42084400	Enhancers	Primary hematopoietic stem cells	blood
10	chr15:42080600-42083400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr15:42080600-42083400	Enhancers	Brain Angular Gyrus	brain
12	chr15:42080600-42083600	Enhancers	Small Intestine	intestine
13	chr15:42080600-42083800	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr15:42080600-42084000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr15:42080600-42084000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr15:42080600-42084000	Enhancers	Primary T cells from cord blood	blood
17	chr15:42080600-42084000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr15:42080600-42084000	Enhancers	Brain Cingulate Gyrus	brain
19	chr15:42080600-42084000	Enhancers	Brain Hippocampus Middle	brain
20	chr15:42080600-42084000	Enhancers	Gastric	stomach
21	chr15:42080600-42084000	Enhancers	Stomach Mucosa	stomach
22	chr15:42080600-42084200	Enhancers	Brain Anterior Caudate	brain
23	chr15:42080600-42084200	Enhancers	Brain Substantia Nigra	brain
24	chr15:42080600-42084600	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr15:42080600-42085000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr15:42080600-42085000	Enhancers	Right Ventricle	heart
27	chr15:42080600-42085200	Enhancers	Left Ventricle	heart
28	chr15:42080600-42086600	Enhancers	Ovary	ovary
29	chr15:42080600-42086800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:42080600-42088200	Enhancers	NHDF-Ad	bronchial
31	chr15:42080800-42083800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr15:42080800-42084000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr15:42080800-42084000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:42080800-42084000	Enhancers	Colon Smooth Muscle	Colon
35	chr15:42081000-42083800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr15:42081000-42084000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:42081000-42084000	Enhancers	Thymus	Thymus
38	chr15:42081000-42084600	Enhancers	Adipose Nuclei	Adipose
39	chr15:42081000-42085000	Enhancers	Fetal Thymus	thymus
40	chr15:42081000-42091800	Enhancers	Placenta	Placenta
41	chr15:42081200-42083600	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr15:42081200-42083800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:42081200-42083800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:42081200-42083800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr15:42081200-42084000	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr15:42081200-42084000	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr15:42081200-42084000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:42081200-42084000	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr15:42081200-42084000	Enhancers	Dnd41	blood
50	chr15:42081200-42084200	Enhancers	HSMMtube	muscle

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