Variant report

Variant	rs10003496
Chromosome Location	chr4:99197839-99197840
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:99190517..99192752-chr4:99196803..99199545,2	MCF-7	breast:
2	chr4:99180773..99182396-chr4:99197532..99199081,2	K562	blood:
3	chr4:99192442..99194622-chr4:99197664..99200193,4	K562	blood:

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10001137	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003061	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10006734	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10010260	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10013248	1.00[ASW][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10015953	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10017075	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10017827	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10022073	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10025311	0.94[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10026222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10027925	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10029895	1.00[ASW][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10032785	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10034649	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10050289	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10212883	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1024127	1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12331722	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12509125	1.00[TSI][hapmap]
rs13353633	0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16996571	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027340	0.87[EUR][1000 genomes]
rs17027388	0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17027393	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027526	0.87[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027538	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027559	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027596	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027597	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027607	1.00[TSI][hapmap]
rs17027617	1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28373747	1.00[EUR][1000 genomes]
rs28374939	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28407050	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28438716	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28446845	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28451188	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28455818	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28459325	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28464398	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28472340	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28478192	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28494643	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28497963	0.91[AMR][1000 genomes]
rs28503871	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28529663	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28558542	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28564255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28589745	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28647503	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28649922	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28651612	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28664868	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28705201	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28731135	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28786730	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28806635	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28807427	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28840158	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28882140	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28883979	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28893208	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275691	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275693	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41525749	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55993060	0.87[EUR][1000 genomes]
rs56805018	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59725407	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60281573	0.87[EUR][1000 genomes]
rs60544326	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60638903	0.87[EUR][1000 genomes]
rs61485715	0.87[EUR][1000 genomes]
rs6831386	0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6834495	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6858042	1.00[AMR][1000 genomes]
rs73832142	0.87[EUR][1000 genomes]
rs73832145	0.87[EUR][1000 genomes]
rs73832149	0.87[EUR][1000 genomes]
rs73832156	0.87[EUR][1000 genomes]
rs73832317	1.00[EUR][1000 genomes]
rs73834403	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834429	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834444	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834475	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834479	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834489	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7655622	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7656868	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7658383	1.00[ASW][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9307226	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9991668	1.00[ASW][hapmap];1.00[GIH][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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994467	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9995184	1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997337	1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997973	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9998801	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9999779	1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv1001570	chr4:98976239-99239838	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1004616	chr4:99085875-99308901	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv879652	chr4:99125659-99303633	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv528127	chr4:99146436-99229839	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv879653	chr4:99152631-99260423	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99183600-99198200	Weak transcription	Ovary	ovary
2	chr4:99183600-99205400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:99184000-99205800	Weak transcription	Gastric	stomach
4	chr4:99184000-99210400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:99184000-99239600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:99184200-99199000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:99184200-99205800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:99184200-99205800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:99184200-99210000	Weak transcription	HSMMtube	muscle
10	chr4:99184200-99242200	Weak transcription	A549	lung
11	chr4:99184600-99205800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:99184600-99211800	Weak transcription	NHLF	lung
13	chr4:99185000-99199600	Weak transcription	NHDF-Ad	bronchial
14	chr4:99185000-99204400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:99185000-99206600	Weak transcription	NH-A	brain
16	chr4:99185200-99205600	Weak transcription	HMEC	breast
17	chr4:99185400-99239400	Weak transcription	NHEK	skin
18	chr4:99186200-99205800	Weak transcription	HUVEC	blood vessel
19	chr4:99186600-99210000	Weak transcription	K562	blood
20	chr4:99187000-99202800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:99189600-99204200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:99191800-99199400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:99192000-99205800	Weak transcription	Psoas Muscle	Psoas
24	chr4:99194000-99215400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr4:99194400-99204200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr4:99194400-99205800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:99194400-99206000	Weak transcription	Aorta	Aorta
28	chr4:99194600-99214600	Weak transcription	Liver	Liver
29	chr4:99196000-99204400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr4:99196200-99198400	Strong transcription	Primary B cells from cord blood	blood
31	chr4:99196400-99204000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr4:99196600-99214200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr4:99197000-99214600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:99197200-99198000	Weak transcription	Dnd41	blood
35	chr4:99197200-99198400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:99197200-99198600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:99197400-99198400	Strong transcription	HSMM	muscle
38	chr4:99197400-99200400	Weak transcription	Fetal Muscle Leg	muscle
39	chr4:99197400-99202600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr4:99197400-99204000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:99197400-99205000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:99197400-99205800	Weak transcription	Left Ventricle	heart
43	chr4:99197400-99210000	Weak transcription	Fetal Thymus	thymus
44	chr4:99197600-99198000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:99197600-99204000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr4:99197600-99205800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:99197600-99210000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr4:99197600-99210000	Weak transcription	Primary T cells from cord blood	blood
49	chr4:99197800-99198000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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