Variant report

Variant	rs766968
Chromosome Location	chr3:112291878-112291879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112285735..112289374-chr3:112291760..112294225,3	K562	blood:
2	chr3:112285735..112288489-chr3:112291503..112294225,2	K562	blood:
3	chr3:112281244..112282995-chr3:112290178..112292787,2	K562	blood:
4	chr3:112290282..112294480-chr3:112295112..112298665,4	K562	blood:
5	chr3:112289268..112293035-chr3:112358216..112361029,3	MCF-7	breast:
6	chr3:112290552..112292970-chr3:112296828..112298665,2	K562	blood:
7	chr3:112291247..112293623-chr3:112708463..112710312,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163607	Chromatin interaction
ENSG00000272844	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000138459	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10755071	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11489073	0.82[EUR][1000 genomes]
rs11706550	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12632867	0.82[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1386895	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1398091	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs1512005	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1512006	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1533159	0.86[GIH][hapmap]
rs1844089	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1873571	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs1877363	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1994713	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2101632	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2131008	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2172196	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2279532	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280066	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2464611	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2633555	0.84[EUR][1000 genomes]
rs2633562	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs2633574	0.86[GIH][hapmap]
rs2633578	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][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];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][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];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2638017	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2638022	0.84[ASW][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2638026	0.86[GIH][hapmap]
rs2638031	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638035	0.86[GIH][hapmap]
rs2638037	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs2638039	0.83[CHB][hapmap]
rs2638042	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2638045	0.80[AMR][1000 genomes]
rs2668217	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2668220	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2668222	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2668223	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2705507	0.86[GIH][hapmap]
rs2705517	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705521	0.86[GIH][hapmap]
rs2705531	0.89[EUR][1000 genomes]
rs2705532	0.83[EUR][1000 genomes]
rs2705534	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs2705543	0.88[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];0.81[GIH][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	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2933134	0.86[GIH][hapmap]
rs2933135	0.86[GIH][hapmap]
rs2933142	0.82[ASN][1000 genomes]
rs2952319	0.86[GIH][hapmap]
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]
rs2952327	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2969896	0.86[GIH][hapmap]
rs2971204	0.82[CEU][hapmap]
rs34233684	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732815	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682410	0.94[ASW][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[YRI][hapmap]
rs4682413	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5000995	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6438079	0.88[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.85[YRI][hapmap]
rs6772077	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6774355	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6792947	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7625366	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7652377	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];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs9288954	0.89[AFR][1000 genomes];0.91[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	0.94[AFR][1000 genomes];0.86[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];0.88[AFR][1000 genomes];0.83[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];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9869455	0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869579	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998036	0.80[GIH][hapmap]

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
rs766968	SLC35A5	cis	Nerve Tibial	GTEx
rs766968	SLC35A5	cis	lymphoblastoid	seeQTL
rs766968	SLC35A5	cis	multi-tissue	Pritchard
rs766968	SLC35A5	cis	Lymphoblastoid	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112281800-112299400	Weak transcription	Left Ventricle	heart
2	chr3:112281800-112301600	Weak transcription	HepG2	liver
3	chr3:112281800-112312000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:112281800-112315400	Weak transcription	Pancreas	Pancrea
5	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
6	chr3:112281800-112325400	Weak transcription	Gastric	stomach
7	chr3:112282000-112312200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
10	chr3:112282200-112303400	Weak transcription	Psoas Muscle	Psoas
11	chr3:112282400-112299400	Weak transcription	Fetal Stomach	stomach
12	chr3:112282400-112301600	Weak transcription	Hela-S3	cervix
13	chr3:112282400-112304400	Weak transcription	Fetal Heart	heart
14	chr3:112282400-112306600	Weak transcription	Right Ventricle	heart
15	chr3:112282400-112307200	Weak transcription	Small Intestine	intestine
16	chr3:112282400-112312400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:112282400-112316800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:112282400-112322800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:112282400-112324200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:112282600-112297200	Weak transcription	Thymus	Thymus
22	chr3:112282600-112298200	Weak transcription	NHEK	skin
23	chr3:112282600-112301200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:112282600-112301400	Weak transcription	A549	lung
25	chr3:112282600-112306800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:112282800-112292600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:112282800-112298600	Weak transcription	Brain Angular Gyrus	brain
28	chr3:112282800-112301400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:112282800-112302200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:112283000-112299200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:112283000-112301800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:112283000-112316400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr3:112283600-112295800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:112283800-112295400	Strong transcription	Liver	Liver
35	chr3:112284000-112297600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:112284000-112298600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:112284200-112293600	Strong transcription	Fetal Thymus	thymus
38	chr3:112284400-112294400	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:112284600-112294600	Weak transcription	Fetal Intestine Small	intestine
40	chr3:112284800-112294200	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:112285200-112292400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr3:112285200-112293400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:112285200-112294400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:112285200-112294600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:112286200-112294200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr3:112286400-112293000	Strong transcription	Fetal Intestine Large	intestine
47	chr3:112286400-112293600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr3:112286400-112294000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:112286400-112294000	Strong transcription	Fetal Brain Female	brain
50	chr3:112286600-112293400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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