Variant report

Variant	rs2232745
Chromosome Location	chr2:85823632-85823633
allele	C/G/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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 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	chr2:85647963..85650741-chr2:85821196..85824176,3	K562	blood:
4	chr2:85785429..85790468-chr2:85820934..85826927,9	MCF-7	breast:
5	chr1:145381800..145384680-chr2:85821996..85823962,2	MCF-7	breast:
6	chr2:85764454..85770994-chr2:85819148..85831427,14	K562	blood:
7	chr2:85777446..85780419-chr2:85822995..85825315,2	MCF-7	breast:
8	chr2:85781595..85783590-chr2:85822310..85824885,2	MCF-7	breast:
9	chr12:129308199..129310201-chr2:85822340..85823983,2	MCF-7	breast:
10	chr2:85788313..85790312-chr2:85822619..85824449,2	K562	blood:
11	chr2:85765572..85767946-chr2:85820164..85824365,5	MCF-7	breast:
12	chr2:85788313..85790216-chr2:85821578..85824119,2	K562	blood:
13	chr2:85764018..85768553-chr2:85822883..85829718,12	MCF-7	breast:
14	chr2:85765237..85769549-chr2:85821409..85826975,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000233396	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000139370	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000152292	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];0.81[EUR][1000 genomes]
rs10190428	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10191726	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10302	1.00[EUR][1000 genomes];0.94[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];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13383605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13414982	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs13418207	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs14242	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1446669	0.84[JPT][hapmap]
rs1562322	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1992151	0.81[EUR][1000 genomes]
rs2028898	0.84[JPT][hapmap]
rs2043675	0.84[JPT][hapmap]
rs2118176	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2232747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2232748	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2232750	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]
rs2304564	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2592551	0.84[JPT][hapmap]
rs3024831	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs3198089	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3755009	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3755010	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3755011	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3821020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs3827550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6547629	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs6643	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6733550	0.80[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6743051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.91[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
rs2232745	LOC388969	cis	multi-tissue	Pritchard
rs2232745	VAMP8	cis	lymphoblastoid	seeQTL
rs2232745	hmm28069	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85821400-85823800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr2:85821600-85823800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:85821600-85823800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr2:85821600-85823800	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr2:85821600-85824000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr2:85821800-85823800	Active TSS	H9 Cell Line	embryonic stem cell
7	chr2:85821800-85824000	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr2:85822000-85823800	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:85822200-85824000	Active TSS	Fetal Kidney	kidney
10	chr2:85822400-85823800	Active TSS	HSMMtube	muscle
11	chr2:85822400-85824000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:85822800-85823800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:85822800-85824000	Flanking Active TSS	Colonic Mucosa	Colon
14	chr2:85823000-85823800	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr2:85823000-85823800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr2:85823000-85823800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr2:85823000-85823800	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr2:85823000-85824000	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr2:85823000-85824000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr2:85823000-85824000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr2:85823000-85824000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:85823000-85824000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr2:85823200-85823800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
24	chr2:85823200-85823800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:85823200-85823800	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr2:85823200-85823800	Flanking Active TSS	Osteobl	bone
27	chr2:85823200-85824000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr2:85823200-85824000	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr2:85823200-85824000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:85823200-85824000	Flanking Active TSS	Liver	Liver
31	chr2:85823200-85824000	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr2:85823200-85824000	Flanking Active TSS	Fetal Brain Female	brain
33	chr2:85823200-85824400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr2:85823200-85825000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:85823200-85829200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr2:85823400-85823800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr2:85823400-85823800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:85823400-85823800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:85823400-85823800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:85823400-85823800	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr2:85823400-85823800	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr2:85823400-85823800	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr2:85823400-85823800	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr2:85823400-85823800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:85823400-85823800	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr2:85823400-85823800	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr2:85823400-85823800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr2:85823400-85823800	Flanking Active TSS	Fetal Brain Male	brain
49	chr2:85823400-85823800	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr2:85823400-85823800	Flanking Active TSS	Fetal Lung	lung

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