Variant report

Variant	rs7652377
Chromosome Location	chr3:112282892-112282893
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112281323..112284151-chr3:113775113..113776995,2	K562	blood:
2	chr3:112278745..112284115-chr3:112357887..112361363,11	MCF-7	breast:
3	chr3:112280159..112284151-chr3:113775113..113778230,3	K562	blood:
4	chr3:112280777..112282990-chr3:112288928..112291699,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151576	Chromatin interaction
ENSG00000163617	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000138459	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10755071	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11489073	0.82[EUR][1000 genomes]
rs11706550	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12632867	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1386895	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1398091	0.82[CEU][hapmap]
rs1512005	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1512006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1844089	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1873571	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1877363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1994713	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2101632	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2131008	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2172196	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2279532	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280066	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2464611	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2633555	0.84[EUR][1000 genomes]
rs2633562	0.82[CEU][hapmap]
rs2633578	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2633579	0.82[CEU][hapmap]
rs2633580	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2633582	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2633584	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638016	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2638017	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs2638018	0.81[AMR][1000 genomes]
rs2638022	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2638031	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638037	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs2638039	0.85[CHB][hapmap]
rs2638042	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2638045	0.83[AMR][1000 genomes]
rs2668217	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2668220	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2668222	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2668223	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2705517	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705531	0.89[EUR][1000 genomes]
rs2705532	0.83[EUR][1000 genomes]
rs2705534	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2705543	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705544	0.82[CEU][hapmap]
rs2705559	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2705565	0.82[CEU][hapmap]
rs2705566	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28866814	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2933142	0.82[ASN][1000 genomes]
rs2952323	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2952326	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs2952327	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs2971204	0.82[CEU][hapmap]
rs34233684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732815	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682410	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs4682413	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5000995	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6438079	0.82[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap]
rs6772077	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6774355	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6792947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7625366	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs766968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288952	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs9288954	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9756562	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9809247	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9848054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9854043	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9866734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9869455	0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869579	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS 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	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7652377	SLC35A5	cis	Lymphoblastoid	GTEx
rs7652377	SLC35A5	cis	Adipose Subcutaneous	GTEx
rs7652377	SLC35A5	cis	multi-tissue	Pritchard
rs7652377	SLC35A5	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112278600-112283800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr3:112279400-112283000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr3:112281800-112283800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:112281800-112286200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:112281800-112287000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:112281800-112289800	Weak transcription	HSMMtube	muscle
7	chr3:112281800-112290400	Weak transcription	Lung	lung
8	chr3:112281800-112291400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:112281800-112299400	Weak transcription	Left Ventricle	heart
10	chr3:112281800-112301600	Weak transcription	HepG2	liver
11	chr3:112281800-112312000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:112281800-112315400	Weak transcription	Pancreas	Pancrea
13	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
14	chr3:112281800-112325400	Weak transcription	Gastric	stomach
15	chr3:112282000-112283000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr3:112282000-112283200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:112282000-112284000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:112282000-112285200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:112282000-112287200	Weak transcription	Aorta	Aorta
20	chr3:112282000-112288200	Weak transcription	Ovary	ovary
21	chr3:112282000-112289600	Weak transcription	Colonic Mucosa	Colon
22	chr3:112282000-112312200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
25	chr3:112282200-112283000	Genic enhancers	Primary B cells from cord blood	blood
26	chr3:112282200-112283000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:112282200-112283200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:112282200-112283200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr3:112282200-112283400	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr3:112282200-112284200	Weak transcription	Fetal Thymus	thymus
31	chr3:112282200-112284400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:112282200-112284800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:112282200-112285200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:112282200-112286400	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:112282200-112287200	Weak transcription	HSMM	muscle
36	chr3:112282200-112303400	Weak transcription	Psoas Muscle	Psoas
37	chr3:112282400-112283000	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr3:112282400-112283000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr3:112282400-112283000	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr3:112282400-112283000	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr3:112282400-112283000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:112282400-112283200	Enhancers	Fetal Brain Male	brain
43	chr3:112282400-112283200	Enhancers	Fetal Brain Female	brain
44	chr3:112282400-112283600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr3:112282400-112283600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr3:112282400-112283800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:112282400-112283800	Weak transcription	Liver	Liver
48	chr3:112282400-112284200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:112282400-112284600	Enhancers	Fetal Intestine Large	intestine
50	chr3:112282400-112284600	Enhancers	Fetal Intestine Small	intestine

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