Variant report

Variant	rs1197772
Chromosome Location	chr15:42064541-42064542
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42064035..42067811-chr15:42102222..42105290,4	K562	blood:
2	chr15:42063685..42066999-chr15:42102378..42105267,3	MCF-7	breast:
3	chr15:42010789..42012329-chr15:42064397..42066596,2	K562	blood:
4	chr15:42064299..42065172-chr15:42102196..42103016,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137802	Chromatin interaction
ENSG00000270702	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1008710	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs10152332	0.90[ASN][1000 genomes]
rs10152364	0.90[ASN][1000 genomes]
rs1061354	0.82[EUR][1000 genomes]
rs10775122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs10775123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10775124	0.90[ASN][1000 genomes]
rs1081022	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070345	0.90[ASN][1000 genomes]
rs11070347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs11070350	0.86[EUR][1000 genomes]
rs11632100	0.90[ASN][1000 genomes]
rs11634840	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11855017	0.90[ASN][1000 genomes]
rs1197666	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1197670	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1197704	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs1197768	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1197769	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12441249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12915325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12916992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1648827	0.86[EUR][1000 genomes]
rs1648828	0.86[EUR][1000 genomes]
rs1648829	0.85[EUR][1000 genomes]
rs1648830	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs1648831	0.86[EUR][1000 genomes]
rs1648832	0.86[EUR][1000 genomes]
rs1648833	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs1648834	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1648835	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs1672464	0.86[EUR][1000 genomes]
rs1672465	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1672466	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs16972089	0.93[CEU][hapmap]
rs16972136	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs1867416	0.87[ASN][1000 genomes]
rs1867417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1880937	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1880938	0.93[ASN][1000 genomes]
rs1899819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1899820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs1899821	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1918314	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2009310	0.82[ASN][1000 genomes]
rs2141141	0.90[ASN][1000 genomes]
rs2178004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2250964	0.90[ASN][1000 genomes]
rs2577947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577952	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2577953	0.90[ASN][1000 genomes]
rs2577954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2577955	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2577958	0.93[ASN][1000 genomes]
rs2577959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2605569	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2605570	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2695162	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2695163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2695164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2695166	0.93[ASN][1000 genomes]
rs2695168	0.95[ASN][1000 genomes]
rs2695169	0.92[CEU][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2918051	0.90[ASN][1000 genomes]
rs2925337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2950446	0.86[ASN][1000 genomes]
rs3743028	0.82[ASN][1000 genomes]
rs3784282	0.84[EUR][1000 genomes]
rs4078788	0.84[EUR][1000 genomes]
rs4244585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap]
rs4270151	0.83[ASN][1000 genomes]
rs4371125	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4465584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4923908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4924568	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs4924571	0.90[ASN][1000 genomes]
rs4924572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs57498313	0.86[EUR][1000 genomes]
rs62002069	0.90[ASN][1000 genomes]
rs6493008	0.84[ASN][1000 genomes]
rs6493010	0.81[ASN][1000 genomes]
rs7164209	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7165230	0.86[EUR][1000 genomes]
rs7169496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs7169668	0.90[ASN][1000 genomes]
rs7177911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7178205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8027390	0.90[ASN][1000 genomes]
rs8028886	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8034261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs8038148	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8038783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8039440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs890508	0.86[EUR][1000 genomes]

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	nsv1049514	chr15:41958482-42081210	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv1038894	chr15:42038152-42077452	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1197772	C17orf85	trans	parietal	SCAN
rs1197772	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41972400-42065200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:42025200-42065400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:42045600-42065200	Weak transcription	Stomach Mucosa	stomach
4	chr15:42054800-42065200	Weak transcription	A549	lung
5	chr15:42055000-42065200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:42055200-42064800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:42056400-42066000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:42057600-42066000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:42059000-42065600	Weak transcription	Fetal Brain Male	brain
10	chr15:42059200-42064800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:42059200-42065200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:42059200-42065200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:42059400-42064800	Weak transcription	Dnd41	blood
14	chr15:42059400-42064800	Weak transcription	HMEC	breast
15	chr15:42059400-42065200	Weak transcription	NHEK	skin
16	chr15:42059400-42066000	Weak transcription	Colonic Mucosa	Colon
17	chr15:42059600-42064800	Weak transcription	HSMM	muscle
18	chr15:42059600-42065000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:42059600-42065000	Weak transcription	NHLF	lung
20	chr15:42059600-42065200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr15:42059600-42065200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:42059600-42065200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr15:42059600-42065200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:42059600-42065200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:42059600-42065200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:42059600-42065200	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:42059600-42065200	Weak transcription	Fetal Intestine Small	intestine
28	chr15:42059600-42065400	Weak transcription	Gastric	stomach
29	chr15:42059600-42065400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr15:42059600-42065600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr15:42059600-42065800	Weak transcription	Pancreas	Pancrea
32	chr15:42059600-42066000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:42059600-42066200	Weak transcription	Aorta	Aorta
34	chr15:42059600-42066200	Weak transcription	Lung	lung
35	chr15:42059600-42066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:42059800-42065000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr15:42059800-42065200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr15:42059800-42065200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:42059800-42065200	Weak transcription	Brain Angular Gyrus	brain
40	chr15:42059800-42065200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:42059800-42065200	Weak transcription	HepG2	liver
42	chr15:42059800-42065200	Weak transcription	NHDF-Ad	bronchial
43	chr15:42059800-42065400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:42059800-42065600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:42059800-42065600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:42059800-42065600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr15:42059800-42066000	Weak transcription	Esophagus	oesophagus
48	chr15:42059800-42066200	Weak transcription	Ovary	ovary
49	chr15:42060000-42064800	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr15:42060000-42064800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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