Variant report

Variant	rs2089510
Chromosome Location	chr4:48176223-48176224
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48173412..48176298-chr4:48428298..48430775,2	K562	blood:
2	chr4:48171039..48173617-chr4:48175205..48177661,3	MCF-7	breast:
3	chr4:48174022..48176386-chr4:48181420..48183923,2	K562	blood:
4	chr4:48175041..48176757-chr4:48255815..48257585,2	K562	blood:
5	chr4:48175434..48177430-chr4:48270272..48272228,2	K562	blood:
6	chr4:48175263..48177129-chr4:48197621..48199593,2	K562	blood:

Variant related genes	Relation type
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10027991	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10805164	1.00[JPT][hapmap]
rs10805165	1.00[JPT][hapmap]
rs10938524	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11730441	0.85[JPT][hapmap]
rs11944549	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11945978	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12332001	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12499541	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12502268	0.84[ASN][1000 genomes]
rs12512766	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512837	0.84[ASN][1000 genomes]
rs13104849	1.00[JPT][hapmap]
rs1466991	0.84[ASN][1000 genomes]
rs1466992	0.84[ASN][1000 genomes]
rs1466993	0.84[ASN][1000 genomes]
rs1466994	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1466995	0.82[ASN][1000 genomes]
rs1466996	0.84[ASN][1000 genomes]
rs1507919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16860999	0.85[ASN][1000 genomes]
rs1961974	0.84[ASN][1000 genomes]
rs1961975	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2089509	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2089511	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2243840	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];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271173	1.00[JPT][hapmap]
rs2464502	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2661529	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2661543	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661544	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2661547	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];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2661548	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];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2704399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2704426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2704433	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704435	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2704436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2704439	0.83[GIH][hapmap]
rs3792620	1.00[JPT][hapmap]
rs3792621	1.00[JPT][hapmap]
rs3792622	1.00[JPT][hapmap]
rs3805179	1.00[JPT][hapmap]
rs3805184	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4323077	0.84[ASN][1000 genomes]
rs4392481	0.84[ASN][1000 genomes]
rs4392482	0.84[ASN][1000 genomes]
rs4695339	0.84[ASN][1000 genomes]
rs4695340	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4695341	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[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695342	0.84[ASN][1000 genomes]
rs4695343	0.84[ASN][1000 genomes]
rs4695344	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4695346	0.84[ASN][1000 genomes]
rs4695347	0.84[ASN][1000 genomes]
rs4695348	0.84[ASN][1000 genomes]
rs4695349	0.84[ASN][1000 genomes]
rs4695350	0.84[ASN][1000 genomes]
rs61326763	0.81[ASN][1000 genomes]
rs62309327	0.84[ASN][1000 genomes]
rs6447616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6814443	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6819592	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6845941	1.00[JPT][hapmap]
rs6851861	0.84[ASN][1000 genomes]
rs7654108	0.84[ASN][1000 genomes]
rs7659164	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7668350	0.84[ASN][1000 genomes]
rs7669393	0.84[ASN][1000 genomes]
rs7670351	0.84[ASN][1000 genomes]
rs7671720	0.82[ASN][1000 genomes]
rs7678246	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7689953	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7695902	0.84[ASN][1000 genomes]
rs7696119	0.84[ASN][1000 genomes]
rs7696271	0.84[ASN][1000 genomes]
rs882715	0.95[EUR][1000 genomes];0.90[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	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482316	chr4:48151953-48338746	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1006853	chr4:48164958-48196335	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1011820	chr4:48170669-48186729	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv819982	chr4:48173420-48178259	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1011366	chr4:48173947-48186644	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1005668	chr4:48173947-48186729	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2089510	TEC	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48157800-48181000	Weak transcription	Pancreas	Pancrea
2	chr4:48158400-48180600	Weak transcription	Spleen	Spleen
3	chr4:48158400-48181800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:48158400-48190000	Weak transcription	Aorta	Aorta
5	chr4:48158600-48179200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:48158600-48179400	Weak transcription	Fetal Intestine Small	intestine
7	chr4:48158800-48180200	Weak transcription	Fetal Thymus	thymus
8	chr4:48159400-48177200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:48166400-48179600	Weak transcription	Thymus	Thymus
10	chr4:48169000-48180600	Weak transcription	Esophagus	oesophagus
11	chr4:48169000-48190000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:48170600-48176800	Weak transcription	Liver	Liver
13	chr4:48170600-48181200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr4:48171200-48181600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:48172200-48176600	Weak transcription	Fetal Heart	heart
16	chr4:48172400-48177400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:48172600-48177400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr4:48173400-48177000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:48173800-48188400	Weak transcription	Lung	lung
20	chr4:48174400-48176600	Enhancers	HSMM	muscle
21	chr4:48174400-48178000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr4:48174800-48176400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:48175000-48176400	Enhancers	Osteobl	bone
24	chr4:48175200-48176400	Enhancers	A549	lung
25	chr4:48175200-48176400	Enhancers	NHEK	skin
26	chr4:48175400-48177000	Flanking Active TSS	GM12878-XiMat	blood
27	chr4:48175400-48178800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr4:48175600-48176400	Enhancers	HSMMtube	muscle
29	chr4:48175600-48176600	Enhancers	K562	blood
30	chr4:48175600-48177000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr4:48175600-48177200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:48175600-48178000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr4:48175600-48180600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr4:48175800-48176400	Enhancers	NH-A	brain
35	chr4:48175800-48176800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr4:48175800-48177000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:48175800-48177400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr4:48175800-48191600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr4:48176000-48176400	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr4:48176000-48176600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:48176000-48177000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:48176000-48177200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr4:48176000-48177200	Weak transcription	HUVEC	blood vessel
44	chr4:48176000-48177400	Weak transcription	Right Atrium	heart
45	chr4:48176000-48177400	Weak transcription	HMEC	breast
46	chr4:48176000-48178400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr4:48176000-48180600	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr4:48176000-48185200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr4:48176000-48185200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:48176000-48185400	Weak transcription	H1 Cell Line	embryonic stem cell

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