Variant report

Variant	rs7625247
Chromosome Location	chr3:53854068-53854069
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53853872..53855809-chr3:53924023..53926528,2	K562	blood:

Variant related genes	Relation type
ENSG00000113811	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11130381	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs11714712	0.83[EUR][1000 genomes]
rs12485510	0.93[EUR][1000 genomes]
rs2241807	0.96[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2241808	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2276838	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3774611	0.92[CEU][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs3774614	0.96[CEU][hapmap]
rs6807783	0.85[ASN][1000 genomes]
rs7626693	0.89[CEU][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs877483	0.85[CEU][hapmap];0.88[MEX][hapmap]
rs877484	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs893365	0.82[EUR][1000 genomes]
rs9830723	0.89[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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers 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	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1003204	chr3:53820070-53877149	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1002375	chr3:53822319-53872753	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv876803	chr3:53822893-53889849	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv518466	chr3:53832903-53882663	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv521181	chr3:53833509-53881471	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7625247	RBM6	cis	parietal	SCAN
rs7625247	HEMK1	cis	cerebellum	SCAN
rs7625247	ABHD14A	cis	parietal	SCAN
rs7625247	RFT1	cis	cerebellum	SCAN
rs7625247	CHDH	cis	cerebellum	SCAN
rs7625247	TLR9	cis	cerebellum	SCAN
rs7625247	PDE12	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53839200-53855200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:53839600-53876600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:53841600-53855600	Weak transcription	Right Ventricle	heart
4	chr3:53841600-53855800	Weak transcription	Right Atrium	heart
5	chr3:53842200-53857200	Strong transcription	Fetal Intestine Large	intestine
6	chr3:53842400-53855600	Weak transcription	Fetal Heart	heart
7	chr3:53846600-53879800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:53847000-53856400	Weak transcription	Brain Germinal Matrix	brain
9	chr3:53847000-53862000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:53849000-53857200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr3:53849000-53857800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:53849000-53858200	Strong transcription	Fetal Stomach	stomach
13	chr3:53849000-53858800	Strong transcription	Liver	Liver
14	chr3:53849000-53859200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:53849000-53866800	Weak transcription	Stomach Mucosa	stomach
16	chr3:53849600-53875400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:53850000-53855200	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr3:53850600-53857400	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr3:53850800-53854600	Strong transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:53850800-53858600	Strong transcription	Gastric	stomach
21	chr3:53851000-53854400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:53851000-53858000	Strong transcription	Pancreas	Pancrea
23	chr3:53851200-53854600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:53851200-53857400	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr3:53851200-53858000	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr3:53851400-53854400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:53851400-53855000	Strong transcription	Brain Hippocampus Middle	brain
28	chr3:53851600-53855000	Strong transcription	Brain Cingulate Gyrus	brain
29	chr3:53851600-53856000	Genic enhancers	HepG2	liver
30	chr3:53851600-53858000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:53851800-53854600	Strong transcription	Brain Angular Gyrus	brain
32	chr3:53851800-53854600	Strong transcription	Brain Anterior Caudate	brain
33	chr3:53852000-53854600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:53852000-53856400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:53852000-53857000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:53852200-53855000	Strong transcription	Brain Substantia Nigra	brain
37	chr3:53852400-53865000	Weak transcription	Aorta	Aorta
38	chr3:53852400-53878200	Weak transcription	Hela-S3	cervix
39	chr3:53852600-53854600	Strong transcription	Spleen	Spleen
40	chr3:53852600-53855800	Weak transcription	Fetal Lung	lung
41	chr3:53852800-53854600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:53853000-53854200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:53853000-53858200	Strong transcription	Fetal Intestine Small	intestine
44	chr3:53853000-53858800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:53853200-53867400	Weak transcription	Lung	lung
46	chr3:53853400-53854200	Strong transcription	Esophagus	oesophagus
47	chr3:53853400-53854400	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:53853400-53856600	Enhancers	Fetal Muscle Leg	muscle
49	chr3:53853400-53858200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:53853400-53877200	Weak transcription	Colonic Mucosa	Colon

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