Variant report

Variant	rs2232750
Chromosome Location	chr2:85824468-85824469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85802926..85807956-chr2:85820760..85828546,8	K562	blood:
2	chr2:85645665..85648237-chr2:85822312..85824673,3	MCF-7	breast:
3	chr2:85785429..85790468-chr2:85820934..85826927,9	MCF-7	breast:
4	chr2:85764454..85770994-chr2:85819148..85831427,14	K562	blood:
5	chr2:85777446..85780419-chr2:85822995..85825315,2	MCF-7	breast:
6	chr2:85781595..85783590-chr2:85822310..85824885,2	MCF-7	breast:
7	chr2:85764018..85768553-chr2:85822883..85829718,12	MCF-7	breast:
8	chr2:85765237..85769549-chr2:85821409..85826975,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000152292	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10180770	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10182351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10190428	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10191726	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10302	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1044158	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs1124836	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13383605	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13414982	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs13418207	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs14242	0.90[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1446669	0.84[JPT][hapmap]
rs1562322	0.90[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1992151	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2028898	0.84[JPT][hapmap]
rs2043675	0.84[JPT][hapmap]
rs2118176	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2232745	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];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2232748	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2304564	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2592551	0.84[JPT][hapmap]
rs3024831	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs3198089	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755009	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3755010	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3755011	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821020	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3827550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6547629	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs6643	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];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6733550	0.80[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6743051	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs699664	0.84[JPT][hapmap]
rs762684	0.84[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv992753	chr2:85822210-85825244	Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2232750	LOC388969	cis	multi-tissue	Pritchard
rs2232750	VAMP8	cis	lymphoblastoid	seeQTL
rs2232750	hmm28069	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85823200-85825000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:85823200-85829200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:85823600-85824600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
4	chr2:85823600-85824600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:85823600-85824800	Enhancers	Fetal Heart	heart
6	chr2:85823600-85825000	Genic enhancers	Gastric	stomach
7	chr2:85823600-85829000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:85823800-85824600	Genic enhancers	Brain Angular Gyrus	brain
9	chr2:85823800-85824600	Genic enhancers	Brain Cingulate Gyrus	brain
10	chr2:85823800-85824600	Enhancers	Fetal Brain Male	brain
11	chr2:85823800-85824600	Genic enhancers	Placenta	Placenta
12	chr2:85823800-85824600	Genic enhancers	Placenta Amnion	Placenta Amnion
13	chr2:85823800-85824600	Transcr. at gene 5' and 3'	Dnd41	blood
14	chr2:85823800-85824800	Genic enhancers	Spleen	Spleen
15	chr2:85823800-85825000	Genic enhancers	Primary B cells from cord blood	blood
16	chr2:85823800-85825000	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr2:85823800-85826000	Transcr. at gene 5' and 3'	HepG2	liver
18	chr2:85823800-85828800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:85824000-85824600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:85824000-85824600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr2:85824000-85824600	Genic enhancers	Adipose Nuclei	Adipose
22	chr2:85824000-85824600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr2:85824000-85824600	Genic enhancers	Fetal Stomach	stomach
24	chr2:85824000-85824600	Strong transcription	Ovary	ovary
25	chr2:85824000-85824600	Genic enhancers	Right Ventricle	heart
26	chr2:85824000-85824600	Genic enhancers	GM12878-XiMat	blood
27	chr2:85824000-85824600	Transcr. at gene 5' and 3'	HSMM	muscle
28	chr2:85824000-85824800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:85824000-85824800	Genic enhancers	Primary B cells from peripheral blood	blood
30	chr2:85824000-85824800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:85824000-85824800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr2:85824000-85824800	Genic enhancers	Colon Smooth Muscle	Colon
33	chr2:85824000-85824800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
34	chr2:85824000-85824800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
35	chr2:85824000-85825000	Genic enhancers	Brain Substantia Nigra	brain
36	chr2:85824000-85825000	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
37	chr2:85824000-85825000	Genic enhancers	Thymus	Thymus
38	chr2:85824000-85825000	Genic enhancers	K562	blood
39	chr2:85824000-85825600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr2:85824000-85826200	Genic enhancers	Fetal Intestine Large	intestine
41	chr2:85824000-85826200	Genic enhancers	Fetal Thymus	thymus
42	chr2:85824000-85826600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:85824000-85826800	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr2:85824000-85826800	Strong transcription	Fetal Lung	lung
45	chr2:85824000-85826800	Strong transcription	Left Ventricle	heart
46	chr2:85824000-85827000	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr2:85824000-85827000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:85824000-85827600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:85824000-85827600	Strong transcription	Aorta	Aorta
50	chr2:85824000-85828200	Genic enhancers	Liver	Liver

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