Variant report

Variant	rs3740839
Chromosome Location	chr11:74877004-74877005
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74867339..74870278-chr11:74875624..74878251,3	K562	blood:
2	chr11:74866771..74870278-chr11:74874697..74878251,4	K562	blood:

Variant related genes	Relation type
ENSG00000137491	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10899078	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10899079	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11236356	0.89[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11236357	0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11236358	0.92[ASN][1000 genomes]
rs11236361	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11236365	0.82[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs11827488	0.84[CEU][hapmap]
rs12361277	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12422149	0.81[JPT][hapmap]
rs4100076	0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4397881	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4944073	0.87[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944074	0.82[GIH][hapmap];0.81[JPT][hapmap]
rs4944992	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4944993	0.89[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944994	0.86[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs57073688	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59633704	0.80[AMR][1000 genomes]
rs6592602	0.83[TSI][hapmap]
rs67904312	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67947132	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7125268	0.82[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs72996586	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72998525	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs881217	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs949069	0.91[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054122	chr11:74872792-74895241	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3740839	KCTD21	cis	cerebellum	SCAN
rs3740839	FCHSD2	cis	cerebellum	SCAN
rs3740839	AQP11	cis	cerebellum	SCAN
rs3740839	UVRAG	cis	parietal	SCAN
rs3740839	PGM2L1	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74863600-74885600	Weak transcription	Colon Smooth Muscle	Colon
2	chr11:74864200-74898400	Weak transcription	Esophagus	oesophagus
3	chr11:74870000-74881000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:74870800-74901600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr11:74871400-74886800	Weak transcription	Brain Substantia Nigra	brain
6	chr11:74872200-74885400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:74872400-74883600	Genic enhancers	Fetal Intestine Small	intestine
8	chr11:74872600-74877200	Enhancers	Fetal Muscle Leg	muscle
9	chr11:74872800-74878200	Enhancers	Fetal Muscle Trunk	muscle
10	chr11:74872800-74878800	Genic enhancers	Fetal Intestine Large	intestine
11	chr11:74873200-74877800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:74873400-74879400	Weak transcription	Adipose Nuclei	Adipose
13	chr11:74874000-74878000	Weak transcription	Gastric	stomach
14	chr11:74874000-74885800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:74875400-74878200	Weak transcription	Stomach Mucosa	stomach
16	chr11:74875400-74885800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:74875600-74885400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr11:74875800-74877800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr11:74875800-74878400	Genic enhancers	Duodenum Mucosa	Duodenum
20	chr11:74875800-74885600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:74876000-74878000	Weak transcription	Left Ventricle	heart
22	chr11:74876000-74885800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr11:74876200-74877600	Weak transcription	Lung	lung
24	chr11:74876200-74877800	Weak transcription	Colonic Mucosa	Colon
25	chr11:74876200-74878000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr11:74876200-74878000	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr11:74876200-74878800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr11:74876200-74879200	Enhancers	HepG2	liver
29	chr11:74876200-74879800	Weak transcription	Right Ventricle	heart
30	chr11:74876200-74880000	Weak transcription	Small Intestine	intestine
31	chr11:74876200-74880200	Weak transcription	Pancreas	Pancrea
32	chr11:74876200-74884200	Weak transcription	Brain Hippocampus Middle	brain
33	chr11:74876200-74886000	Weak transcription	Fetal Thymus	thymus
34	chr11:74876200-74906200	Weak transcription	Spleen	Spleen
35	chr11:74876400-74882400	Genic enhancers	Liver	Liver
36	chr11:74876600-74877200	Genic enhancers	Fetal Stomach	stomach
37	chr11:74876800-74877800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:74876800-74878800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr11:74876800-74879800	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links