Variant report

Variant	rs2929408
Chromosome Location	chr3:20082969-20082970
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20082249..20087148-chr3:20090873..20095169,4	K562	blood:
2	chr3:20036427..20038510-chr3:20080865..20083451,2	K562	blood:
3	chr3:19986985..19992254-chr3:20079680..20083856,14	K562	blood:
4	chr3:19987513..19990087-chr3:20080861..20083140,3	MCF-7	breast:
5	chr3:19986921..19992254-chr3:20078952..20084327,16	K562	blood:

Variant related genes	Relation type
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction
ENSG00000201545	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2623074	0.87[CHB][hapmap];0.82[YRI][hapmap]
rs2929387	0.82[YRI][hapmap]
rs2948080	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
11	esv3396791	chr3:20080148-20083246	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	esv3426803	chr3:20080473-20083321	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2929408	EFHB	cis	parietal	SCAN
rs2929408	EFHB	cis	cerebellum	SCAN
rs2929408	RAB5A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20080000-20083200	Active TSS	Aorta	Aorta
2	chr3:20080200-20083200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:20080200-20083200	Active TSS	Left Ventricle	heart
4	chr3:20080200-20083200	Active TSS	Ovary	ovary
5	chr3:20080200-20083200	Active TSS	NHLF	lung
6	chr3:20080200-20083400	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr3:20080200-20083400	Active TSS	Colon Smooth Muscle	Colon
8	chr3:20080400-20083200	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr3:20080400-20083200	Active TSS	Fetal Brain Female	brain
10	chr3:20080400-20083200	Active TSS	Fetal Kidney	kidney
11	chr3:20080400-20083200	Active TSS	Rectal Smooth Muscle	rectum
12	chr3:20080400-20083400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:20080400-20083400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:20080400-20083400	Active TSS	Psoas Muscle	Psoas
15	chr3:20080400-20083600	Active TSS	Right Ventricle	heart
16	chr3:20080400-20083800	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr3:20080600-20083000	Active TSS	Duodenum Mucosa	Duodenum
18	chr3:20080600-20083200	Active TSS	Brain Substantia Nigra	brain
19	chr3:20080600-20083200	Active TSS	Lung	lung
20	chr3:20080600-20083200	Active TSS	Stomach Mucosa	stomach
21	chr3:20080600-20083200	Active TSS	GM12878-XiMat	blood
22	chr3:20080600-20083200	Active TSS	NHDF-Ad	bronchial
23	chr3:20080600-20083400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:20080600-20083400	Active TSS	Thymus	Thymus
25	chr3:20080600-20083600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:20080800-20083200	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr3:20080800-20083200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:20080800-20083200	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr3:20080800-20083200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:20080800-20083200	Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr3:20080800-20083200	Active TSS	Brain Angular Gyrus	brain
32	chr3:20080800-20083200	Active TSS	Fetal Intestine Large	intestine
33	chr3:20080800-20083200	Active TSS	Fetal Intestine Small	intestine
34	chr3:20080800-20083200	Active TSS	Fetal Muscle Leg	muscle
35	chr3:20080800-20083400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:20080800-20083400	Active TSS	Brain Hippocampus Middle	brain
37	chr3:20080800-20083600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:20080800-20084400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:20081000-20083000	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr3:20081000-20083000	Active TSS	Primary monocytes fromperipheralblood	blood
41	chr3:20081000-20083000	Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr3:20081000-20083000	Active TSS	HSMMtube	muscle
43	chr3:20081000-20083200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:20081000-20083200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:20081000-20083200	Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr3:20081000-20083200	Active TSS	Muscle Satellite Cultured Cells	--
47	chr3:20081000-20083200	Active TSS	Brain Anterior Caudate	brain
48	chr3:20081000-20083200	Active TSS	Fetal Lung	lung
49	chr3:20081000-20083200	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr3:20081000-20083400	Active TSS	Brain Cingulate Gyrus	brain

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