Variant report

Variant	rs7643293
Chromosome Location	chr3:121449612-121449613
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121449098..121450770-chr3:121467330..121469547,2	MCF-7	breast:
2	chr3:121449263..121451677-chr3:121468938..121471042,2	K562	blood:

Variant related genes	Relation type
ENSG00000173230	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10470412	1.00[CEU][hapmap]
rs10511407	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs10934556	0.89[EUR][1000 genomes]
rs10934557	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10934561	1.00[CEU][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap]
rs11915822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11919421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12486456	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap]
rs12488717	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489110	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489196	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12489686	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap]
rs12491109	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap]
rs12491671	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12492214	1.00[CEU][hapmap];0.85[JPT][hapmap];0.93[YRI][hapmap]
rs12492861	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap]
rs12493927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12629720	1.00[CEU][hapmap]
rs12631803	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12636562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637265	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13321798	1.00[CEU][hapmap]
rs1574654	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814668	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1881997	0.91[CEU][hapmap]
rs1881998	0.91[CEU][hapmap]
rs1919553	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1919554	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1919556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1920307	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs1971281	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055034	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2689278	1.00[CEU][hapmap]
rs2700413	1.00[CEU][hapmap]
rs2700414	0.85[JPT][hapmap]
rs35674179	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35825165	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3805125	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs3805129	0.90[CEU][hapmap];0.85[JPT][hapmap]
rs3966063	0.81[EUR][1000 genomes]
rs3966068	0.81[YRI][hapmap]
rs4048693	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41271407	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4610269	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs4676761	1.00[CEU][hapmap]
rs55930520	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55964762	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56109033	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56286202	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6438681	1.00[CEU][hapmap]
rs6762575	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766737	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6775634	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6786605	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793556	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6798575	0.91[CEU][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620562	0.91[CEU][hapmap]
rs7625960	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7626052	1.00[CEU][hapmap]
rs7640859	0.81[CEU][hapmap]
rs7650341	1.00[CEU][hapmap]
rs9818194	0.82[YRI][hapmap]
rs9834185	1.00[CEU][hapmap]
rs9859243	0.81[YRI][hapmap]
rs9869891	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS 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 target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7643293	HCLS1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121429000-121450000	Strong transcription	Rectal Mucosa Donor 29	rectum
2	chr3:121430200-121450000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:121430600-121450000	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr3:121430800-121450000	Strong transcription	Fetal Intestine Large	intestine
5	chr3:121431000-121450000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:121431000-121450000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr3:121431400-121449800	Strong transcription	Duodenum Mucosa	Duodenum
8	chr3:121431400-121450400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:121432600-121449800	Strong transcription	Fetal Muscle Leg	muscle
10	chr3:121436600-121466600	Weak transcription	Stomach Mucosa	stomach
11	chr3:121437800-121450000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:121438400-121449800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr3:121438400-121450000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:121439400-121467200	Weak transcription	Small Intestine	intestine
15	chr3:121443400-121464800	Weak transcription	Fetal Brain Male	brain
16	chr3:121444200-121449800	Strong transcription	Placenta	Placenta
17	chr3:121444600-121449800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:121444600-121455200	Weak transcription	Psoas Muscle	Psoas
19	chr3:121444600-121466400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:121444800-121450200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:121444800-121450200	Weak transcription	Left Ventricle	heart
22	chr3:121444800-121450600	Weak transcription	Fetal Brain Female	brain
23	chr3:121444800-121457200	Weak transcription	Gastric	stomach
24	chr3:121444800-121457200	Weak transcription	Right Ventricle	heart
25	chr3:121444800-121457400	Weak transcription	Pancreas	Pancrea
26	chr3:121444800-121458800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:121444800-121458800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:121444800-121466400	Weak transcription	Colonic Mucosa	Colon
29	chr3:121444800-121467200	Weak transcription	Aorta	Aorta
30	chr3:121444800-121467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:121444800-121467400	Weak transcription	Spleen	Spleen
32	chr3:121445200-121449800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:121445200-121457200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:121445200-121457800	Weak transcription	Lung	lung
35	chr3:121445200-121466200	Weak transcription	Fetal Intestine Small	intestine
36	chr3:121445200-121466800	Weak transcription	Thymus	Thymus
37	chr3:121445200-121467400	Weak transcription	Esophagus	oesophagus
38	chr3:121445800-121467000	Weak transcription	Fetal Stomach	stomach
39	chr3:121445800-121467400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:121446000-121451800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:121446800-121450400	Strong transcription	Primary T cells from cord blood	blood
42	chr3:121447400-121456800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:121447600-121467000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:121447800-121449800	Weak transcription	HSMMtube	muscle
45	chr3:121447800-121452400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:121447800-121466400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr3:121447800-121467000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr3:121448000-121449800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr3:121448000-121449800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:121448000-121453400	Weak transcription	A549	lung

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