Variant report

Variant	rs2638026
Chromosome Location	chr3:112271213-112271214
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112270877..112274678-chr3:112278992..112281610,4	MCF-7	breast:
2	chr3:112270443..112273330-chr3:112277844..112281278,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144848	Chromatin interaction
ENSG00000138459	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1105938	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1155073	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12632867	0.81[CHB][hapmap]
rs1386895	0.81[CHB][hapmap]
rs1398091	0.81[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs1488259	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1512006	0.86[GIH][hapmap]
rs1533159	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1601852	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1814052	0.91[ASN][1000 genomes]
rs1844089	0.81[CHB][hapmap]
rs1873571	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs1873572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1877363	0.86[GIH][hapmap]
rs2171513	0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2171514	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2292442	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2633562	0.84[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2633574	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2633575	0.90[ASN][1000 genomes]
rs2633578	0.81[CHB][hapmap]
rs2633579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[ASN][1000 genomes]
rs2633580	0.81[CHB][hapmap]
rs2633582	0.81[CHB][hapmap]
rs2633588	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2633589	0.91[ASN][1000 genomes]
rs2638013	0.91[ASN][1000 genomes]
rs2638015	0.91[ASN][1000 genomes]
rs2638016	0.81[CHB][hapmap]
rs2638017	0.81[CHB][hapmap]
rs2638019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638022	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2638023	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2638027	0.89[AMR][1000 genomes]
rs2638028	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638031	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2638032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638037	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2638039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2668215	0.86[AMR][1000 genomes]
rs2668219	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705505	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2705507	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2705515	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705518	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705521	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][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]
rs2705522	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705525	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2705533	0.82[ASN][1000 genomes]
rs2705534	0.81[CHB][hapmap]
rs2705535	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2705536	0.82[ASN][1000 genomes]
rs2705541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2705544	0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2705548	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2705552	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2705556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705559	0.81[CHB][hapmap]
rs2705560	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705562	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2705564	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705565	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.89[ASN][1000 genomes]
rs2705566	0.85[CHB][hapmap]
rs2933134	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2933135	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2933137	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2942061	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2952319	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2952320	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2952323	0.81[CHB][hapmap]
rs2952324	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2952325	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952326	0.81[CHB][hapmap]
rs2952327	0.81[CHB][hapmap]
rs2969895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2969896	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2971204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3112268	0.89[ASN][1000 genomes]
rs6792947	0.86[GIH][hapmap]
rs728568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs751875	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs766968	0.86[GIH][hapmap]
rs766969	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9869455	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs9869579	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs998036	0.88[ASW][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2638026	SLC35A5	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112234200-112272000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:112239600-112272200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:112243000-112271600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr3:112244400-112274200	Weak transcription	Stomach Mucosa	stomach
5	chr3:112244400-112278200	Weak transcription	K562	blood
6	chr3:112244400-112278400	Weak transcription	HSMMtube	muscle
7	chr3:112245200-112273200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:112245800-112279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:112247600-112279600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:112248400-112274200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:112249200-112275800	Weak transcription	Fetal Stomach	stomach
12	chr3:112249200-112276000	Weak transcription	Spleen	Spleen
13	chr3:112249200-112278200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:112249200-112278400	Weak transcription	Aorta	Aorta
15	chr3:112249200-112279600	Weak transcription	Esophagus	oesophagus
16	chr3:112249200-112279600	Weak transcription	Gastric	stomach
17	chr3:112249200-112279800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:112249400-112276200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:112249400-112279600	Weak transcription	Lung	lung
20	chr3:112251000-112274200	Weak transcription	Brain Angular Gyrus	brain
21	chr3:112252600-112278400	Weak transcription	Fetal Kidney	kidney
22	chr3:112253000-112273400	Weak transcription	Brain Substantia Nigra	brain
23	chr3:112253200-112278600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:112254200-112273600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:112257600-112274000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr3:112260000-112278200	Weak transcription	Fetal Brain Male	brain
27	chr3:112260400-112279600	Weak transcription	Pancreas	Pancrea
28	chr3:112265000-112276000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:112266000-112274200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:112266200-112278200	Weak transcription	Fetal Heart	heart
31	chr3:112266200-112278200	Weak transcription	NHLF	lung
32	chr3:112266200-112278400	Weak transcription	Colonic Mucosa	Colon
33	chr3:112266400-112278200	Weak transcription	NHEK	skin
34	chr3:112266800-112274400	Weak transcription	A549	lung
35	chr3:112266800-112278400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:112267000-112274000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:112267000-112274000	Weak transcription	HUVEC	blood vessel
38	chr3:112267000-112274600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:112267000-112278400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:112267000-112278400	Weak transcription	NHDF-Ad	bronchial
41	chr3:112267200-112274200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:112267200-112276000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:112267200-112276000	Weak transcription	Fetal Muscle Leg	muscle
44	chr3:112267200-112278400	Weak transcription	Thymus	Thymus
45	chr3:112267200-112279200	Weak transcription	Right Ventricle	heart
46	chr3:112267400-112271400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:112267400-112274400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:112267600-112273000	Weak transcription	Brain Anterior Caudate	brain
49	chr3:112267600-112273000	Weak transcription	Brain Hippocampus Middle	brain
50	chr3:112267600-112274800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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