Variant report

Variant	rs869332
Chromosome Location	chr7:102632247-102632248
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:159480769..159481581-chr7:102631646..102632292,2	Hela-S3	cervix:
2	chr7:102627919..102629951-chr7:102630613..102632281,3	K562	blood:
3	chr7:102631511..102633980-chr7:102714406..102717077,3	K562	blood:
4	chr7:102629921..102632610-chr7:102634773..102637196,3	K562	blood:
5	chr7:102628465..102631626-chr7:102631792..102634551,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161040	Chromatin interaction
ENSG00000170632	Chromatin interaction
ENSG00000250588	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10228495	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs10241865	0.95[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs10242028	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10250490	0.83[ASN][1000 genomes]
rs10271157	0.81[ASN][1000 genomes]
rs10271184	0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]
rs10273725	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs10279449	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs10808120	1.00[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1100046	0.86[ASN][1000 genomes]
rs11514917	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11768949	0.86[ASN][1000 genomes]
rs11972261	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11976237	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11978799	0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs11981980	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs12537977	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs12666317	0.86[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs12668434	0.86[CHB][hapmap];0.93[CHD][hapmap]
rs13221585	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13222980	0.85[ASN][1000 genomes]
rs13232194	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs13233521	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs13242493	0.82[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs1541519	0.90[CHB][hapmap];0.93[CHD][hapmap]
rs1608651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17136090	0.86[CHB][hapmap];0.93[CHD][hapmap]
rs1829957	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2190673	0.80[ASN][1000 genomes]
rs2222539	0.88[ASN][1000 genomes]
rs2228686	0.90[ASN][1000 genomes]
rs2298854	0.82[ASN][1000 genomes]
rs2411059	0.87[ASN][1000 genomes]
rs28856331	0.84[ASN][1000 genomes]
rs41501847	0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs4296965	0.87[ASN][1000 genomes]
rs4609128	0.90[ASN][1000 genomes]
rs4620204	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs4729860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4729866	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4729873	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs6465876	0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs6465878	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs6465880	0.81[ASN][1000 genomes]
rs6945997	0.89[ASN][1000 genomes]
rs6946773	0.86[CHB][hapmap];0.93[CHD][hapmap]
rs6947403	0.86[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs6953980	0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs6960428	0.95[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs6963104	0.84[TSI][hapmap]
rs6978630	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7458786	0.89[ASN][1000 genomes]
rs7779145	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs7780405	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7780981	0.86[CHB][hapmap];0.93[CHD][hapmap]
rs7782908	0.81[CHB][hapmap]
rs7785272	1.00[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs7789252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7794668	0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs7800548	0.95[CHB][hapmap];0.90[CHD][hapmap]
rs7807055	0.90[ASN][1000 genomes]
rs847646	0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs847647	0.86[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap]
rs847648	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs847649	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs847656	0.86[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs847658	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs952879	0.84[ASN][1000 genomes]
rs955992	0.99[ASN][1000 genomes]
rs9718453	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv5881	chr7:102610488-102655699	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs869332	LRRC17	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102623800-102636600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:102625800-102632600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:102629000-102634200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr7:102629000-102634400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr7:102629400-102633400	Enhancers	Pancreas	Pancrea
6	chr7:102629400-102633600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:102629600-102632600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr7:102630200-102632400	Weak transcription	Left Ventricle	heart
9	chr7:102630200-102632600	Weak transcription	Aorta	Aorta
10	chr7:102630200-102632600	Weak transcription	Gastric	stomach
11	chr7:102630400-102633600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:102630400-102634600	Enhancers	Osteobl	bone
13	chr7:102630400-102635400	Enhancers	HUVEC	blood vessel
14	chr7:102630600-102633800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:102630600-102634200	Enhancers	HMEC	breast
16	chr7:102630800-102634600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:102631000-102633400	Enhancers	Small Intestine	intestine
18	chr7:102631000-102634200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr7:102631000-102634200	Enhancers	NHDF-Ad	bronchial
20	chr7:102631000-102634200	Enhancers	NHEK	skin
21	chr7:102631000-102634400	Enhancers	NHLF	lung
22	chr7:102631200-102633200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:102631200-102633400	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr7:102631200-102634200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:102631200-102634200	Enhancers	Primary hematopoietic stem cells	blood
26	chr7:102631200-102634400	Enhancers	Colon Smooth Muscle	Colon
27	chr7:102631200-102634400	Enhancers	Stomach Mucosa	stomach
28	chr7:102631200-102634600	Enhancers	NH-A	brain
29	chr7:102631200-102634800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:102631400-102633800	Enhancers	HepG2	liver
31	chr7:102631400-102634200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:102631400-102634400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr7:102631600-102632600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr7:102631600-102633600	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr7:102631600-102633800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr7:102631600-102634200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr7:102631600-102634200	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr7:102631600-102634200	Enhancers	HSMM	muscle
39	chr7:102631800-102632800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr7:102631800-102633000	Enhancers	HSMMtube	muscle
41	chr7:102631800-102633200	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr7:102631800-102634000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr7:102631800-102634200	Enhancers	Duodenum Mucosa	Duodenum
44	chr7:102631800-102634200	Enhancers	Rectal Smooth Muscle	rectum
45	chr7:102631800-102634200	Flanking Active TSS	A549	lung
46	chr7:102632000-102632600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:102632000-102633400	Flanking Active TSS	Hela-S3	cervix
48	chr7:102632000-102633600	Enhancers	Fetal Kidney	kidney
49	chr7:102632000-102633600	Enhancers	Ovary	ovary
50	chr7:102632000-102634400	Flanking Active TSS	K562	blood

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