Variant report

Variant	rs2638597
Chromosome Location	chr3:120049292-120049293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:120046370..120050212-chr3:120051068..120055542,4	K562	blood:
2	chr3:120047936..120052812-chr3:120065943..120070052,5	K562	blood:
3	chr3:120048937..120051112-chr3:120133444..120135223,2	K562	blood:
4	chr3:120047929..120050381-chr3:120059244..120062451,3	MCF-7	breast:
5	chr3:120042251..120044176-chr3:120048760..120051015,2	K562	blood:
6	chr3:120045375..120049014-chr3:120049152..120052143,4	MCF-7	breast:
7	chr3:120048008..120050106-chr3:120067294..120069387,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163428	Chromatin interaction
ENSG00000240661	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10048964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1085614	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1085616	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1085617	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1147681	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147689	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147690	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147697	0.81[AMR][1000 genomes]
rs11914405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928731	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13318758	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13318838	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13327125	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1625178	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1700	0.84[CEU][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs1716855	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716856	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1733326	1.00[CEU][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1733328	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28600057	1.00[ASN][1000 genomes]
rs28826066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62266319	1.00[ASN][1000 genomes]
rs6764516	1.00[CEU][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]
rs6767308	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777979	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799005	0.84[ASW][hapmap];0.84[CEU][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes]
rs6808913	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622363	0.94[LWK][hapmap]
rs787186	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs787187	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs787189	0.87[EUR][1000 genomes]
rs787190	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs787192	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs787193	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs787196	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs787200	0.87[EUR][1000 genomes]
rs787205	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787206	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787207	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787208	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs809792	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs923729	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951658	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810151	0.81[AMR][1000 genomes]
rs9810784	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822759	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851711	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9856670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860676	0.84[ASW][hapmap];0.84[CEU][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs9876547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2638597	B4GALT4	cis	parietal	SCAN
rs2638597	PARP15	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120026600-120060800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:120026800-120067200	Weak transcription	Aorta	Aorta
3	chr3:120031000-120055600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:120033200-120050000	Weak transcription	Spleen	Spleen
5	chr3:120033200-120060400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:120033200-120060400	Weak transcription	Pancreas	Pancrea
7	chr3:120033200-120067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:120034600-120052400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:120035200-120049800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:120036600-120053600	Weak transcription	Fetal Heart	heart
11	chr3:120037200-120052200	Weak transcription	Brain Anterior Caudate	brain
12	chr3:120038800-120049800	Weak transcription	Fetal Brain Female	brain
13	chr3:120038800-120051600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:120039200-120053600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:120039600-120049400	Weak transcription	NHLF	lung
16	chr3:120039800-120049400	Weak transcription	Fetal Intestine Large	intestine
17	chr3:120040400-120049800	Weak transcription	Brain Angular Gyrus	brain
18	chr3:120040400-120055000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:120040400-120056400	Strong transcription	Dnd41	blood
20	chr3:120041000-120049600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:120041000-120056200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:120041000-120057400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:120041000-120057400	Weak transcription	Small Intestine	intestine
24	chr3:120041000-120058000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:120041200-120052400	Weak transcription	NHEK	skin
26	chr3:120041400-120049600	Weak transcription	Brain Substantia Nigra	brain
27	chr3:120041600-120051000	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:120041600-120055200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:120042800-120060400	Weak transcription	Gastric	stomach
30	chr3:120042800-120060600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:120043000-120049400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:120043000-120050000	Weak transcription	Psoas Muscle	Psoas
33	chr3:120043000-120050000	Weak transcription	Thymus	Thymus
34	chr3:120043000-120054000	Weak transcription	Fetal Intestine Small	intestine
35	chr3:120043200-120051600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:120043200-120060400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:120043400-120049600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:120043400-120049800	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:120044000-120054400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:120044400-120052000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr3:120044400-120066800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:120044600-120055400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:120045200-120054200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:120045200-120066800	Weak transcription	Stomach Mucosa	stomach
45	chr3:120045600-120054200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:120045600-120054600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:120045600-120066800	Weak transcription	Colonic Mucosa	Colon
48	chr3:120045800-120052400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:120045800-120054400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:120045800-120054800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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