Variant report

Variant	rs2298914
Chromosome Location	chr1:171710405-171710406
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:171710341..171715416-chr1:171748571..171752440,7	MCF-7	breast:
2	chr1:171708496..171713095-chr1:171747641..171752422,13	MCF-7	breast:
3	chr1:171453211..171456610-chr1:171708836..171712780,4	K562	blood:
4	chr1:171709343..171715185-chr1:171748592..171756289,15	K562	blood:
5	chr1:171710254..171714548-chr1:171728803..171733052,4	K562	blood:
6	chr1:171709554..171712819-chr1:171724332..171729197,5	K562	blood:
7	chr1:171710037..171714996-chr1:171734843..171738629,6	MCF-7	breast:
8	chr1:171614558..171616177-chr1:171708966..171711154,2	MCF-7	breast:
9	chr1:171709564..171713750-chr1:171736602..171743117,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000271459	Chromatin interaction
ENSG00000010165	Chromatin interaction
ENSG00000117523	Chromatin interaction
ENSG00000236741	Chromatin interaction
ENSG00000253060	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1001373	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10489249	1.00[CEU][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10489251	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1052676	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10903	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10913489	0.82[EUR][1000 genomes]
rs10913490	0.82[EUR][1000 genomes]
rs10913492	0.82[EUR][1000 genomes]
rs10913511	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10913514	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10913529	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10913565	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913578	0.83[JPT][hapmap]
rs10913582	1.00[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10913587	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11576221	1.00[CEU][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs11577073	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11577197	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11577745	1.00[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11578179	0.93[EUR][1000 genomes]
rs11578699	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11578723	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11579698	0.94[EUR][1000 genomes]
rs11580415	0.94[EUR][1000 genomes]
rs11580522	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11583920	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11590680	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11590714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11799420	0.82[EUR][1000 genomes]
rs11799938	0.81[CHD][hapmap]
rs11801846	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11803174	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11808099	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11811780	0.83[EUR][1000 genomes]
rs12119232	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12123727	0.81[EUR][1000 genomes]
rs12127026	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12128536	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12132221	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs15655	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16843251	0.83[JPT][hapmap]
rs17649050	1.00[CEU][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17649068	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17649250	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2421911	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3753539	0.81[GIH][hapmap];0.83[JPT][hapmap]
rs3766653	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55670848	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58455759	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6656003	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6659874	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6662720	1.00[CEU][hapmap]
rs6667559	1.00[CEU][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs6669263	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6670427	1.00[CEU][hapmap]
rs6678890	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6679354	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7528057	0.81[EUR][1000 genomes]
rs7536436	0.94[EUR][1000 genomes]
rs7536543	0.94[EUR][1000 genomes]
rs9661596	0.82[EUR][1000 genomes]
rs9662506	1.00[CEU][hapmap]
rs9662853	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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 miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2298914	VAMP4	cis	lymphoblastoid	seeQTL
rs2298914	PRDX6	cis	parietal	SCAN
rs2298914	VAMP4	cis	multi-tissue	Pritchard
rs2298914	BCHE	trans	lymphoblastoid	seeQTL
rs2298914	MAEL	cis	cerebellum	SCAN
rs2298914	VAMP4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171708400-171710600	Flanking Active TSS	NH-A	brain
2	chr1:171708800-171712600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:171708800-171712800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:171709200-171710600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:171709200-171710600	Flanking Active TSS	Dnd41	blood
6	chr1:171709200-171712200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:171709200-171712400	Active TSS	NHLF	lung
8	chr1:171709400-171712400	Active TSS	NHDF-Ad	bronchial
9	chr1:171709400-171712600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:171709600-171710600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr1:171709600-171710800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:171709800-171710600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:171709800-171710600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr1:171709800-171710600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:171709800-171710600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr1:171709800-171710600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr1:171709800-171710600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:171709800-171710600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:171709800-171710600	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr1:171709800-171710600	Flanking Active TSS	Fetal Brain Female	brain
21	chr1:171709800-171710600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr1:171709800-171710600	Flanking Active TSS	HMEC	breast
23	chr1:171709800-171710800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:171709800-171710800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr1:171709800-171712400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:171709800-171712600	Active TSS	Aorta	Aorta
27	chr1:171709800-171712600	Active TSS	Psoas Muscle	Psoas
28	chr1:171710000-171710600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr1:171710000-171710600	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr1:171710000-171710600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr1:171710000-171710600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr1:171710000-171710600	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr1:171710000-171710600	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr1:171710000-171710600	Flanking Active TSS	Fetal Heart	heart
35	chr1:171710000-171710600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr1:171710000-171710600	Flanking Active TSS	Rectal Smooth Muscle	rectum
37	chr1:171710000-171710600	Flanking Active TSS	HUVEC	blood vessel
38	chr1:171710000-171710800	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr1:171710000-171711000	Active TSS	Right Atrium	heart
40	chr1:171710000-171711800	Active TSS	Primary T cells fromperipheralblood	blood
41	chr1:171710000-171712000	Active TSS	Brain Angular Gyrus	brain
42	chr1:171710000-171712400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:171710000-171712600	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr1:171710000-171712600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:171710000-171712600	Active TSS	Stomach Smooth Muscle	stomach
46	chr1:171710000-171713000	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr1:171710000-171713000	Active TSS	Fetal Brain Male	brain
48	chr1:171710200-171710600	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:171710200-171710600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr1:171710200-171710600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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