Variant report

Variant	rs2814990
Chromosome Location	chr6:34612379-34612380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34611223..34612801-chr6:34622555..34624943,2	K562	blood:
2	chr6:34610887..34612849-chr6:34723663..34725571,2	MCF-7	breast:
3	chr6:34608904..34611557-chr6:34612149..34614331,2	K562	blood:
4	chr6:34610138..34612719-chr6:34663419..34665445,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196821	Chromatin interaction
ENSG00000272288	Chromatin interaction
ENSG00000124562	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11970421	0.94[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs16894102	0.94[CHB][hapmap]
rs1964810	0.94[ASN][1000 genomes]
rs2064253	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2092344	0.81[YRI][hapmap]
rs2235571	0.90[ASN][1000 genomes]
rs2235572	0.94[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2252551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294536	0.87[ASN][1000 genomes]
rs2492862	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2744937	0.81[YRI][hapmap]
rs2744942	0.81[YRI][hapmap]
rs2744948	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2744952	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744953	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2744954	0.81[YRI][hapmap]
rs2744955	0.81[YRI][hapmap]
rs2744962	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2744963	0.94[CEU][hapmap];0.94[CHB][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2744964	0.81[YRI][hapmap]
rs2744966	0.94[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2744967	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2744968	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2744970	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2744971	0.81[YRI][hapmap]
rs2744972	0.81[YRI][hapmap]
rs2744975	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2744977	0.81[YRI][hapmap]
rs2764199	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[EUR][1000 genomes]
rs2814943	0.81[YRI][hapmap]
rs2814950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs2814954	0.81[EUR][1000 genomes]
rs2814983	0.81[YRI][hapmap]
rs2814985	0.81[YRI][hapmap]
rs2814989	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2814993	0.81[YRI][hapmap]
rs2814996	0.81[YRI][hapmap]
rs2814997	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2814998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815000	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2815003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815005	0.81[YRI][hapmap]
rs3736896	0.81[ASN][1000 genomes]
rs3798349	0.94[CHB][hapmap]
rs3800455	0.83[ASN][1000 genomes]
rs3800456	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3800457	0.81[YRI][hapmap]
rs41438444	0.87[ASN][1000 genomes]
rs4615374	0.92[ASN][1000 genomes]
rs4618513	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711399	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4713823	0.81[ASN][1000 genomes]
rs56987113	0.97[ASN][1000 genomes]
rs57994417	0.88[ASN][1000 genomes]
rs58643640	0.94[ASN][1000 genomes]
rs6906500	0.81[EUR][1000 genomes]
rs6932930	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6939345	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs73413893	0.85[ASN][1000 genomes]
rs7751664	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7752237	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7772600	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9296126	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9368829	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9380451	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv830640	chr6:34542489-34714677	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv885794	chr6:34561585-34673149	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv1032557	chr6:34565802-34802008	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised 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	33 gene(s)	inside rSNPs	diseases
11	nsv538196	chr6:34565802-34802008	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	esv2763967	chr6:34566255-34925463	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
13	nsv1020710	chr6:34607214-34890143	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2814990	UHRF1BP1	cis	Artery Tibial	GTEx
rs2814990	UHRF1BP1	cis	Whole Blood	GTEx
rs2814990	UHRF1BP1	cis	Adipose Subcutaneous	GTEx
rs2814990	C6orf107	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34557400-34612400	Weak transcription	Fetal Kidney	kidney
2	chr6:34567800-34612400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:34570400-34612600	Weak transcription	Brain Anterior Caudate	brain
4	chr6:34570800-34618800	Weak transcription	Brain Angular Gyrus	brain
5	chr6:34571000-34621400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:34571000-34624000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:34572400-34612600	Weak transcription	Aorta	Aorta
8	chr6:34574400-34612400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:34574400-34623400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr6:34574600-34612600	Weak transcription	Gastric	stomach
11	chr6:34574600-34613600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:34574600-34613600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:34574800-34612400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr6:34574800-34612400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:34574800-34612600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:34574800-34613200	Weak transcription	Small Intestine	intestine
17	chr6:34575000-34612400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:34575000-34612400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:34575000-34612600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:34575000-34618800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:34577400-34613400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr6:34577400-34618600	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:34578800-34612400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:34579200-34614200	Weak transcription	Pancreas	Pancrea
25	chr6:34579800-34612600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:34582800-34613200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr6:34584400-34613000	Weak transcription	Esophagus	oesophagus
28	chr6:34586000-34624200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:34587400-34624200	Weak transcription	Spleen	Spleen
30	chr6:34590400-34612400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:34593000-34623600	Weak transcription	Colonic Mucosa	Colon
32	chr6:34596800-34613200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr6:34597800-34613400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:34598000-34620000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:34598200-34612600	Weak transcription	HUVEC	blood vessel
36	chr6:34598600-34614200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:34598800-34612400	Weak transcription	Primary B cells from cord blood	blood
38	chr6:34598800-34619200	Weak transcription	NH-A	brain
39	chr6:34598800-34623200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr6:34599200-34614200	Weak transcription	NHLF	lung
41	chr6:34599400-34613400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr6:34599400-34615200	Weak transcription	Left Ventricle	heart
43	chr6:34599400-34616200	Weak transcription	Psoas Muscle	Psoas
44	chr6:34599600-34614200	Weak transcription	A549	lung
45	chr6:34599600-34618600	Weak transcription	HMEC	breast
46	chr6:34601000-34612800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:34603600-34612600	Weak transcription	Lung	lung
48	chr6:34603600-34624000	Weak transcription	Brain Germinal Matrix	brain
49	chr6:34603600-34625800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:34603800-34612600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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