Variant report

Variant	rs542784
Chromosome Location	chr11:75092187-75092188
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:75062379..75064704-chr11:75090478..75092323,2	MCF-7	breast:
2	chr11:75090369..75092612-chr11:75094388..75097255,4	MCF-7	breast:
3	chr11:75090671..75094563-chr11:75095690..75099742,4	K562	blood:

Variant related genes	Relation type
ENSG00000137486	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11236417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11236420	0.86[ASN][1000 genomes]
rs12363921	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2510894	0.82[CEU][hapmap]
rs3016302	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3016304	0.86[ASN][1000 genomes]
rs473233	0.95[ASN][1000 genomes]
rs473961	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs475099	0.91[ASN][1000 genomes]
rs475161	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs477625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs477783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs477837	0.82[CEU][hapmap]
rs478777	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs489691	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs515343	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs518115	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs521455	0.96[ASN][1000 genomes]
rs532279	0.92[ASN][1000 genomes]
rs536516	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs536538	0.86[ASN][1000 genomes]
rs542944	0.86[ASN][1000 genomes]
rs546715	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs552129	0.97[ASN][1000 genomes]
rs555875	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs567647	0.92[ASN][1000 genomes]
rs575781	0.92[ASN][1000 genomes]
rs576508	0.95[ASN][1000 genomes]
rs580152	0.91[ASN][1000 genomes]
rs582477	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs598062	0.85[ASN][1000 genomes]
rs598936	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs613248	0.86[ASN][1000 genomes]
rs627133	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs629991	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs630429	0.87[ASN][1000 genomes]
rs646360	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs654079	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs658573	0.82[CEU][hapmap]
rs663235	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs672534	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs677106	0.92[CEU][hapmap]
rs686020	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041640	chr11:74945824-75174688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
2	nsv832211	chr11:74945839-75106125	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
3	nsv897920	chr11:75087520-75181249	Genic enhancers Bivalent Enhancer Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv993873	chr11:75090965-75093952	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75081200-75095200	Weak transcription	Dnd41	blood
2	chr11:75083600-75094200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr11:75083800-75099400	Weak transcription	Right Atrium	heart
4	chr11:75087400-75099400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:75089800-75092400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:75089800-75092600	Enhancers	Fetal Intestine Large	intestine
7	chr11:75089800-75093000	Enhancers	Fetal Intestine Small	intestine
8	chr11:75090200-75092200	Enhancers	Fetal Stomach	stomach
9	chr11:75090200-75092400	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr11:75090200-75092800	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr11:75090400-75096000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr11:75090800-75092200	Enhancers	Duodenum Mucosa	Duodenum
13	chr11:75090800-75092200	Enhancers	Stomach Smooth Muscle	stomach
14	chr11:75090800-75093000	Enhancers	Placenta	Placenta
15	chr11:75091000-75092400	Enhancers	Fetal Heart	heart
16	chr11:75091000-75092400	Enhancers	Fetal Muscle Leg	muscle
17	chr11:75091200-75093000	Enhancers	Stomach Mucosa	stomach
18	chr11:75091400-75092200	Enhancers	HSMM	muscle
19	chr11:75091400-75092400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr11:75091400-75092400	Enhancers	A549	lung
21	chr11:75091400-75094200	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr11:75091400-75096000	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr11:75091600-75092200	Enhancers	HSMMtube	muscle
24	chr11:75091600-75092400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:75091600-75092400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:75091600-75092400	Enhancers	Primary hematopoietic stem cells	blood
27	chr11:75091600-75092400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr11:75091600-75092400	Enhancers	K562	blood
29	chr11:75091600-75092600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:75091600-75092600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:75091800-75092200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr11:75091800-75092200	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr11:75091800-75092200	Enhancers	Liver	Liver
34	chr11:75091800-75092200	Enhancers	Pancreas	Pancrea
35	chr11:75091800-75092200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr11:75091800-75092200	Enhancers	Hela-S3	cervix
37	chr11:75091800-75092200	Flanking Bivalent TSS/Enh	HepG2	liver
38	chr11:75091800-75092400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr11:75091800-75092400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr11:75091800-75092400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:75091800-75092400	Enhancers	Colonic Mucosa	Colon
42	chr11:75091800-75092400	Enhancers	Esophagus	oesophagus
43	chr11:75091800-75092400	Enhancers	Fetal Muscle Trunk	muscle
44	chr11:75091800-75092400	Enhancers	Spleen	Spleen
45	chr11:75091800-75093000	Enhancers	Lung	lung
46	chr11:75092000-75092200	Enhancers	Fetal Thymus	thymus
47	chr11:75092000-75092400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:75092000-75092400	Enhancers	Adipose Nuclei	Adipose
49	chr11:75092000-75092400	Enhancers	Colon Smooth Muscle	Colon
50	chr11:75092000-75092400	Enhancers	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links