Variant report

Variant	rs2040349
Chromosome Location	chr2:85889525-85889526
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85886964..85889940-chr2:85892432..85895474,3	K562	blood:
2	chr2:85886740..85890485-chr2:85890962..85895474,8	K562	blood:
3	chr2:85886996..85889867-chr2:85891019..85894482,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168878	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10206961	0.82[GIH][hapmap]
rs1044158	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs12463933	0.82[CEU][hapmap];0.88[TSI][hapmap]
rs13406807	0.82[EUR][1000 genomes]
rs2118177	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[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];1.00[ASN][1000 genomes]
rs2232748	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs58588820	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62166774	0.84[EUR][1000 genomes]
rs6547629	0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs6733550	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes]
rs7607208	0.84[EUR][1000 genomes]
rs9678632	0.82[EUR][1000 genomes]
rs9752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv874464	chr2:85886175-85898898	Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2040349	GGCX	cis	parietal	SCAN
rs2040349	VAMP8	cis	lymphoblastoid	seeQTL
rs2040349	VAMP8	cis	uninvolved skin	skin_eQTL
rs2040349	GGCX	cis	cerebellum	SCAN
rs2040349	hmm28069	cis	multi-tissue	Pritchard

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85876600-85895400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:85877000-85890000	Weak transcription	Ovary	ovary
3	chr2:85877200-85893200	Weak transcription	Brain Substantia Nigra	brain
4	chr2:85877800-85890200	Weak transcription	Small Intestine	intestine
5	chr2:85878800-85891400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:85879400-85890200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:85879400-85890200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:85879600-85889800	Weak transcription	Fetal Intestine Large	intestine
9	chr2:85879600-85894000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:85879600-85896000	Weak transcription	GM12878-XiMat	blood
11	chr2:85880400-85891800	Weak transcription	HepG2	liver
12	chr2:85880600-85889600	Weak transcription	Brain Germinal Matrix	brain
13	chr2:85880600-85890200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:85880600-85890200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:85880800-85889800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:85880800-85890200	Weak transcription	K562	blood
17	chr2:85881400-85891000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:85881600-85890200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:85881800-85895800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:85882400-85890400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr2:85883600-85890400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:85883600-85892800	Weak transcription	Fetal Lung	lung
23	chr2:85883600-85900000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:85883800-85890000	Weak transcription	HMEC	breast
25	chr2:85883800-85890200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr2:85883800-85890200	Weak transcription	HSMM	muscle
27	chr2:85884000-85889600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:85884200-85890200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:85884800-85891000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:85884800-85895600	Weak transcription	Primary B cells from cord blood	blood
31	chr2:85884800-85896600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:85886400-85890600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:85886400-85893200	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:85886400-85901000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:85886600-85890800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:85887000-85891600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:85887000-85892600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:85887000-85896200	Weak transcription	Fetal Brain Female	brain
39	chr2:85887000-85905800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:85887200-85890200	Weak transcription	Gastric	stomach
41	chr2:85887200-85890400	Weak transcription	Esophagus	oesophagus
42	chr2:85887200-85891400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:85887200-85895200	Weak transcription	Fetal Thymus	thymus
44	chr2:85887400-85891400	Weak transcription	Fetal Intestine Small	intestine
45	chr2:85887400-85893600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:85887800-85890800	Enhancers	HUVEC	blood vessel
47	chr2:85888000-85889600	Enhancers	Fetal Muscle Trunk	muscle
48	chr2:85888000-85889600	Enhancers	Stomach Smooth Muscle	stomach
49	chr2:85888000-85890000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:85888000-85890400	Enhancers	Placenta	Placenta

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