Variant report

Variant	rs7624303
Chromosome Location	chr3:157851223-157851224
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:157823071..157825253-chr3:157850410..157852335,2	K562	blood:
2	chr3:157849729..157851539-chr3:157855010..157858229,4	K562	blood:
3	chr3:157849729..157852576-chr3:157856575..157858121,2	K562	blood:

Variant related genes	Relation type
ENSG00000174891	Chromatin interaction
ENSG00000168779	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs11712563	0.86[EUR][1000 genomes]
rs11715599	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11717618	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11719153	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1193511	0.89[CHD][hapmap]
rs12485440	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12486461	0.97[ASN][1000 genomes]
rs12636733	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12696067	0.80[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs13059066	0.86[JPT][hapmap]
rs13061378	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs1581408	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs1608100	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs1608101	0.97[ASN][1000 genomes]
rs1609525	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.99[ASN][1000 genomes]
rs1609526	0.90[ASN][1000 genomes]
rs1610266	0.97[ASN][1000 genomes]
rs1610267	0.97[ASN][1000 genomes]
rs1610268	0.97[ASN][1000 genomes]
rs1729998	0.86[JPT][hapmap]
rs1730032	0.86[JPT][hapmap]
rs17683939	1.00[CEU][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs1851062	1.00[CEU][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs1915935	0.85[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs1918000	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2139696	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2693540	0.93[CHD][hapmap]
rs2693546	0.86[JPT][hapmap]
rs4261830	0.99[ASN][1000 genomes]
rs4317053	0.94[ASN][1000 genomes]
rs4346508	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4414801	0.94[ASN][1000 genomes]
rs4431056	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs4602343	0.97[ASN][1000 genomes]
rs4622858	0.99[ASN][1000 genomes]
rs4642075	0.95[ASN][1000 genomes]
rs4680411	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs4680412	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4680413	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680421	1.00[CEU][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4680425	0.83[EUR][1000 genomes]
rs4680428	0.83[EUR][1000 genomes]
rs57665991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60962704	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6441174	0.97[ASN][1000 genomes]
rs6772246	0.82[EUR][1000 genomes]
rs6773505	0.90[ASN][1000 genomes]
rs6784968	0.83[EUR][1000 genomes]
rs6789448	0.99[ASN][1000 genomes]
rs6790608	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs6794461	0.92[ASN][1000 genomes]
rs6797626	0.90[ASN][1000 genomes]
rs6800218	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6803532	0.94[ASN][1000 genomes]
rs6803630	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs6807468	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs696715	0.86[JPT][hapmap]
rs698975	0.86[JPT][hapmap]
rs698976	0.86[JPT][hapmap]
rs698981	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs698982	0.86[JPT][hapmap]
rs698992	0.96[CHD][hapmap];0.86[JPT][hapmap]
rs699918	0.86[JPT][hapmap]
rs73164102	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73166358	0.88[EUR][1000 genomes]
rs73168723	0.86[EUR][1000 genomes]
rs73168799	0.86[EUR][1000 genomes]
rs73170303	0.84[EUR][1000 genomes]
rs73170306	0.83[EUR][1000 genomes]
rs73170310	0.83[EUR][1000 genomes]
rs7614572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7617666	0.81[CEU][hapmap]
rs7622971	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7630176	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7647342	1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs827104	0.96[CHD][hapmap];0.86[JPT][hapmap]
rs827130	0.93[CHD][hapmap]
rs827139	0.96[CHD][hapmap];0.86[JPT][hapmap]
rs827141	0.96[CHD][hapmap];0.86[JPT][hapmap]
rs827142	0.86[JPT][hapmap]
rs827153	0.86[JPT][hapmap]
rs827155	0.86[JPT][hapmap]
rs827160	0.86[JPT][hapmap]
rs827162	0.93[CHD][hapmap]
rs827168	0.93[CHD][hapmap]
rs827170	0.86[JPT][hapmap]
rs827173	0.96[CHD][hapmap];0.86[JPT][hapmap]
rs827801	0.86[JPT][hapmap]
rs827805	0.86[JPT][hapmap]
rs862352	0.86[JPT][hapmap]
rs864331	0.86[JPT][hapmap]
rs866657	0.86[JPT][hapmap]
rs9290020	0.90[ASN][1000 genomes]
rs9290021	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9814942	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9820954	0.99[ASN][1000 genomes]
rs9848433	0.95[ASN][1000 genomes]
rs9862337	0.81[ASN][1000 genomes]
rs9870745	0.96[ASN][1000 genomes]
rs9871021	0.80[ASN][1000 genomes]
rs9881063	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv829768	chr3:157832878-158012070	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7624303	RSRC1	Cis_1M	lymphoblastoid	RTeQTL
rs7624303	SMC4	cis	cerebellum	SCAN
rs7624303	SLC33A1	cis	cerebellum	SCAN
rs7624303	RP11-538P18.2	cis	Skin Sun Exposed Lower leg	GTEx
rs7624303	RP11-538P18.2	cis	lung	GTEx
rs7624303	RSRC1	cis	uninvolved skin	skin_eQTL
rs7624303	RP11-538P18.2	cis	Artery Tibial	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157828600-157857000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:157829200-157861400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:157830000-157866400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:157833200-157856200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:157836000-157851600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:157836600-157854600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:157837600-157877600	Weak transcription	Fetal Heart	heart
8	chr3:157838800-157862600	Weak transcription	Pancreas	Pancrea
9	chr3:157840200-157856000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:157840800-157856200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr3:157842800-157851800	Weak transcription	Brain Germinal Matrix	brain
12	chr3:157842800-157855600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:157842800-157855600	Weak transcription	Fetal Stomach	stomach
14	chr3:157842800-157855800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:157842800-157856400	Weak transcription	Placenta	Placenta
16	chr3:157842800-157856800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:157842800-157858000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:157842800-157858200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:157843000-157868600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr3:157843400-157856600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:157843600-157857200	Weak transcription	HepG2	liver
22	chr3:157843600-157866200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr3:157843600-157886800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:157845800-157854200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:157845800-157857600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:157846000-157851600	Weak transcription	Fetal Kidney	kidney
27	chr3:157846000-157851800	Weak transcription	Fetal Brain Male	brain
28	chr3:157846000-157851800	Weak transcription	Osteobl	bone
29	chr3:157846000-157857400	Weak transcription	Spleen	Spleen
30	chr3:157846000-157860800	Weak transcription	Small Intestine	intestine
31	chr3:157846000-157868400	Weak transcription	Lung	lung
32	chr3:157846000-157869200	Weak transcription	Esophagus	oesophagus
33	chr3:157846200-157855800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:157846200-157857200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:157846200-157857200	Weak transcription	Brain Substantia Nigra	brain
36	chr3:157846200-157857400	Weak transcription	NHDF-Ad	bronchial
37	chr3:157846200-157857600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:157846200-157857800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:157846200-157859200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:157846200-157861800	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:157846200-157862800	Weak transcription	Fetal Brain Female	brain
42	chr3:157846200-157869200	Weak transcription	Psoas Muscle	Psoas
43	chr3:157846200-157869200	Weak transcription	NHEK	skin
44	chr3:157846200-157872000	Weak transcription	Primary T cells from cord blood	blood
45	chr3:157846200-157875200	Weak transcription	Gastric	stomach
46	chr3:157846200-157893400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:157846200-157893600	Weak transcription	Aorta	Aorta
48	chr3:157846600-157855800	Weak transcription	Hela-S3	cervix
49	chr3:157846600-157858000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:157846600-157867400	Weak transcription	Rectal Mucosa Donor 31	rectum

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