Variant report

Variant	rs2241807
Chromosome Location	chr3:53857158-53857159
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs11130381	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11714712	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12485510	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2241808	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3774611	0.89[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3774614	0.92[CEU][hapmap]
rs7625247	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]
rs7626693	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[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];0.99[ASN][1000 genomes]
rs877483	0.89[CEU][hapmap];0.84[MEX][hapmap]
rs877484	0.89[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs893365	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9001	0.84[CHB][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2241807	HEMK1	cis	cerebellum	SCAN
rs2241807	PDE12	cis	parietal	SCAN
rs2241807	ABHD14A	cis	parietal	SCAN
rs2241807	TLR9	cis	cerebellum	SCAN
rs2241807	IL17RB	Cis_1M	lymphoblastoid	RTeQTL
rs2241807	RFT1	cis	cerebellum	SCAN
rs2241807	RBM6	cis	parietal	SCAN
rs2241807	CHDH	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53839600-53876600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:53842200-53857200	Strong transcription	Fetal Intestine Large	intestine
3	chr3:53846600-53879800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:53847000-53862000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:53849000-53857200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr3:53849000-53857800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:53849000-53858200	Strong transcription	Fetal Stomach	stomach
8	chr3:53849000-53858800	Strong transcription	Liver	Liver
9	chr3:53849000-53859200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:53849000-53866800	Weak transcription	Stomach Mucosa	stomach
11	chr3:53849600-53875400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:53850600-53857400	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr3:53850800-53858600	Strong transcription	Gastric	stomach
14	chr3:53851000-53858000	Strong transcription	Pancreas	Pancrea
15	chr3:53851200-53857400	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr3:53851200-53858000	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr3:53851600-53858000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:53852400-53865000	Weak transcription	Aorta	Aorta
19	chr3:53852400-53878200	Weak transcription	Hela-S3	cervix
20	chr3:53853000-53858200	Strong transcription	Fetal Intestine Small	intestine
21	chr3:53853000-53858800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:53853200-53867400	Weak transcription	Lung	lung
23	chr3:53853400-53858200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:53853400-53877200	Weak transcription	Colonic Mucosa	Colon
25	chr3:53853600-53861800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:53853600-53866800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:53853800-53879000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:53854000-53879400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:53854200-53871600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:53854200-53877400	Weak transcription	Esophagus	oesophagus
31	chr3:53854400-53858000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:53854400-53873000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:53854400-53876400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:53854600-53858000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:53854600-53859600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr3:53854600-53862600	Weak transcription	Brain Anterior Caudate	brain
37	chr3:53854600-53866600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:53854600-53867400	Weak transcription	Spleen	Spleen
39	chr3:53854600-53873200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:53855600-53857200	Enhancers	Fetal Muscle Trunk	muscle
41	chr3:53855800-53862000	Weak transcription	Brain Substantia Nigra	brain
42	chr3:53856000-53858800	Strong transcription	HepG2	liver
43	chr3:53856200-53859000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:53856200-53866000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:53856400-53857800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:53856600-53857800	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:53856600-53857800	Weak transcription	GM12878-XiMat	blood
48	chr3:53856600-53862200	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:53856800-53879200	Weak transcription	Ovary	ovary
50	chr3:53857000-53857400	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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