Variant report

Variant	rs13414982
Chromosome Location	chr2:85881464-85881465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85763539..85766353-chr2:85881297..85884242,2	K562	blood:
2	chr2:85879386..85881998-chr2:85891410..85893784,2	MCF-7	breast:
3	chr2:85880829..85882437-chr2:85885388..85887097,2	K562	blood:

Variant related genes	Relation type
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10182351	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs1124836	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs13383605	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs14242	1.00[CEU][hapmap];0.90[GIH][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap]
rs1562322	1.00[CEU][hapmap];0.90[GIH][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap]
rs1992151	0.89[AMR][1000 genomes]
rs2232745	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2232747	1.00[CEU][hapmap]
rs2232750	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs2304564	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs3024821	0.98[ASN][1000 genomes]
rs3024831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3198089	1.00[CEU][hapmap]
rs3755011	1.00[CEU][hapmap]
rs3821020	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes]
rs3827550	1.00[CEU][hapmap]
rs6643	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs6743051	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7316	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs762548	0.97[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	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874461	chr2:85853653-85939207	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Enhancers Active TSS 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	10 gene(s)	inside rSNPs	diseases
4	nsv874462	chr2:85853653-85941074	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874463	chr2:85853653-85946708	Strong transcription Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS 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	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13414982	hmm28069	cis	multi-tissue	Pritchard
rs13414982	VAMP8	cis	lymphoblastoid	seeQTL
rs13414982	LOC388969	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85844800-85881600	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr2:85845000-85881800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:85845000-85883600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:85845400-85886400	Strong transcription	Fetal Muscle Leg	muscle
5	chr2:85845600-85881800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:85845600-85882200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr2:85845800-85881600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:85845800-85881800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:85846000-85887000	Strong transcription	Liver	Liver
10	chr2:85846000-85887400	Strong transcription	Fetal Intestine Small	intestine
11	chr2:85846200-85882000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:85846200-85889400	Strong transcription	Thymus	Thymus
13	chr2:85846800-85881600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:85856200-85881600	Strong transcription	Primary T cells from cord blood	blood
15	chr2:85856200-85882400	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr2:85861600-85883800	Strong transcription	HMEC	breast
17	chr2:85862000-85887200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:85862200-85881600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:85865000-85884000	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr2:85870800-85881600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr2:85873200-85882000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:85873200-85886600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:85876000-85881600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr2:85876400-85888800	Weak transcription	Fetal Heart	heart
25	chr2:85876400-85888800	Weak transcription	Right Atrium	heart
26	chr2:85876600-85885000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr2:85876600-85895400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr2:85876800-85881600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr2:85877000-85889000	Weak transcription	Stomach Mucosa	stomach
30	chr2:85877000-85890000	Weak transcription	Ovary	ovary
31	chr2:85877200-85883000	Weak transcription	Right Ventricle	heart
32	chr2:85877200-85884800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:85877200-85885200	Weak transcription	Brain Angular Gyrus	brain
34	chr2:85877200-85888600	Weak transcription	Aorta	Aorta
35	chr2:85877200-85893200	Weak transcription	Brain Substantia Nigra	brain
36	chr2:85877800-85890200	Weak transcription	Small Intestine	intestine
37	chr2:85878200-85885200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:85878200-85886400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:85878200-85888800	Weak transcription	Brain Anterior Caudate	brain
40	chr2:85878600-85886200	Weak transcription	Esophagus	oesophagus
41	chr2:85878800-85886600	Weak transcription	Gastric	stomach
42	chr2:85878800-85891400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:85879200-85881800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:85879400-85881600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:85879400-85883200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:85879400-85883200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:85879400-85885200	Weak transcription	Fetal Brain Male	brain
48	chr2:85879400-85888000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:85879400-85889200	Weak transcription	Colonic Mucosa	Colon
50	chr2:85879400-85890200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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