Variant report

Variant	rs4938799
Chromosome Location	chr11:120208257-120208258
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:120202465..120204611-chr11:120208153..120210823,2	K562	blood:
2	chr11:120205769..120208609-chr11:120306177..120309218,3	MCF-7	breast:
3	chr11:120207958..120210253-chr11:120247180..120249390,2	K562	blood:
4	chr11:120208182..120211778-chr11:120301083..120304985,6	K562	blood:
5	chr11:120112775..120115205-chr11:120208059..120211030,2	K562	blood:
6	chr11:120187467..120189508-chr11:120207099..120208640,2	MCF-7	breast:
7	chr11:120207370..120208927-chr11:120276135..120278811,2	K562	blood:
8	chr11:120105780..120109103-chr11:120204882..120208710,5	K562	blood:
9	chr11:120105780..120109103-chr11:120204882..120208710,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196914	Chromatin interaction
ENSG00000137709	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10502235	0.90[JPT][hapmap]
rs10750172	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10750173	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10750174	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10790378	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10790380	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10790382	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10790383	0.92[CEU][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs10892562	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10892563	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10892564	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10892566	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10892567	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10892570	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10892574	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10892576	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11217821	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11217840	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11217841	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11217852	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11217874	0.84[JPT][hapmap]
rs11217875	0.89[JPT][hapmap]
rs11600703	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11601535	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs11823300	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11827818	0.84[JPT][hapmap]
rs12361632	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12417581	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12420378	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12787285	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12806740	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1892894	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1893261	0.96[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276035	0.84[JPT][hapmap]
rs2305008	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs2305010	0.81[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs34298380	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36011588	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3809059	0.81[JPT][hapmap]
rs4381380	0.92[CEU][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4539328	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4936517	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4938801	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4938804	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4938805	0.88[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4938806	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4938807	0.90[JPT][hapmap]
rs4938808	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap]
rs496248	0.81[JPT][hapmap]
rs61898351	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs632137	0.81[JPT][hapmap]
rs6589810	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6589811	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6589812	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6589813	0.81[EUR][1000 genomes]
rs7101415	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7104639	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7107211	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7117063	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7117321	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7118391	0.98[GIH][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7121779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7126328	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7126413	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7129944	0.90[JPT][hapmap]
rs7131046	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7131597	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs723937	0.92[CEU][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs7478880	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7924772	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7924963	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7924975	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7932037	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7932658	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7933086	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7937612	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7939137	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs7948928	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7952529	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894839	0.88[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs9633919	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9633950	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv3360321	chr11:120205767-120208715	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4938799	TMEM136	cis	parietal	SCAN
rs4938799	ARHGEF12	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120205600-120208600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr11:120205600-120208800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr11:120205600-120209000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr11:120205600-120209000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr11:120205600-120209400	Active TSS	Brain Hippocampus Middle	brain
6	chr11:120205600-120209400	Active TSS	Fetal Intestine Large	intestine
7	chr11:120205600-120209600	Active TSS	Fetal Muscle Trunk	muscle
8	chr11:120205600-120210000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr11:120205600-120210000	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr11:120205600-120210000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:120205600-120210000	Active TSS	Colon Smooth Muscle	Colon
12	chr11:120205600-120210000	Active TSS	Hela-S3	cervix
13	chr11:120205600-120210200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:120205600-120210200	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr11:120205600-120210200	Active TSS	A549	lung
16	chr11:120205600-120210600	Active TSS	Brain Cingulate Gyrus	brain
17	chr11:120205600-120210800	Active TSS	Colonic Mucosa	Colon
18	chr11:120205600-120211600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:120205800-120208600	Active TSS	Fetal Intestine Small	intestine
20	chr11:120205800-120208800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:120205800-120208800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:120205800-120209000	Active TSS	Pancreas	Pancrea
23	chr11:120205800-120209000	Active TSS	Stomach Mucosa	stomach
24	chr11:120205800-120209400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr11:120205800-120209600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:120205800-120210200	Active TSS	Psoas Muscle	Psoas
27	chr11:120205800-120210200	Active TSS	NHDF-Ad	bronchial
28	chr11:120205800-120210400	Active TSS	Ovary	ovary
29	chr11:120205800-120210800	Active TSS	Aorta	Aorta
30	chr11:120205800-120210800	Active TSS	Brain Angular Gyrus	brain
31	chr11:120205800-120211000	Active TSS	Left Ventricle	heart
32	chr11:120205800-120211200	Active TSS	Right Atrium	heart
33	chr11:120205800-120211600	Active TSS	Right Ventricle	heart
34	chr11:120206000-120209000	Active TSS	H9 Cell Line	embryonic stem cell
35	chr11:120206000-120209600	Active TSS	Placenta	Placenta
36	chr11:120206200-120208400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:120206200-120208600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr11:120206200-120208600	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr11:120206200-120208800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr11:120206200-120208800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:120206200-120209000	Active TSS	Fetal Heart	heart
42	chr11:120206200-120209400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:120206200-120209400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr11:120206200-120209400	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr11:120206200-120209400	Active TSS	Fetal Kidney	kidney
46	chr11:120206200-120209400	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr11:120206200-120209600	Active TSS	H1 Cell Line	embryonic stem cell
48	chr11:120206200-120210000	Active TSS	Muscle Satellite Cultured Cells	--
49	chr11:120206200-120210400	Active TSS	Fetal Stomach	stomach
50	chr11:120206200-120210800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links