Variant report

Variant	rs6741091
Chromosome Location	chr2:20135283-20135284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20101118..20105131-chr2:20134643..20136584,3	K562	blood:
2	chr2:20101403..20102975-chr2:20134094..20136589,2	K562	blood:

Variant related genes	Relation type
ENSG00000271991	Chromatin interaction
ENSG00000183891	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10165128	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10178256	0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[TSI][hapmap]
rs10187524	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10190308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10191437	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10495700	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11096633	0.89[CHD][hapmap]
rs1115274	0.84[ASN][1000 genomes]
rs12477955	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12478934	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12612708	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12616917	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1370587	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1437859	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1595414	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs1595415	0.83[ASN][1000 genomes]
rs1947730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2045779	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2242192	0.81[ASN][1000 genomes]
rs28401180	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28598872	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3731663	0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap]
rs3820949	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4297843	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6721864	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6736663	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7569975	0.94[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7572536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7575732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7584726	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7604699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
3	nsv521619	chr2:20098208-20150817	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv527453	chr2:20109061-20160209	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv1798392	chr2:20131079-20173255	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20102800-20173200	Weak transcription	Fetal Brain Male	brain
2	chr2:20108800-20137400	Weak transcription	Right Ventricle	heart
3	chr2:20114400-20143800	Weak transcription	Brain Substantia Nigra	brain
4	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
5	chr2:20121600-20135800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:20123400-20135800	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:20124800-20142800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:20126400-20137200	Weak transcription	Colonic Mucosa	Colon
9	chr2:20127400-20167800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:20127600-20139200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:20127800-20135800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:20128000-20137400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:20128000-20139200	Weak transcription	Pancreas	Pancrea
14	chr2:20128400-20188400	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:20128400-20189200	Weak transcription	Small Intestine	intestine
16	chr2:20128600-20136000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr2:20129000-20135400	Weak transcription	Brain Germinal Matrix	brain
18	chr2:20129400-20135600	Weak transcription	Primary T cells from cord blood	blood
19	chr2:20129400-20135800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr2:20129400-20135800	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:20129400-20135800	Weak transcription	Fetal Thymus	thymus
22	chr2:20129400-20138600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:20129400-20143000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:20129400-20144000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:20129400-20184800	Weak transcription	Esophagus	oesophagus
26	chr2:20129600-20136000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:20129600-20138000	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:20129600-20149800	Weak transcription	Spleen	Spleen
29	chr2:20129600-20189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:20130200-20136000	Weak transcription	Brain Anterior Caudate	brain
31	chr2:20130200-20189000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:20130400-20135400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:20130400-20135800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:20130400-20135800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:20130400-20136000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:20130400-20136000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:20130400-20136200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:20130400-20140200	Weak transcription	Liver	Liver
39	chr2:20130400-20141800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:20130400-20142000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:20130400-20142600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr2:20130400-20149400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:20130400-20149400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:20130400-20164600	Weak transcription	Lung	lung
45	chr2:20130400-20188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:20130600-20135800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr2:20130600-20135800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr2:20130600-20135800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:20130600-20135800	Weak transcription	Aorta	Aorta
50	chr2:20130600-20135800	Weak transcription	Fetal Intestine Large	intestine

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