Variant report

Variant	rs11229904
Chromosome Location	chr11:59032669-59032670
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	chr11:59032632..59035314-chr11:59038415..59042026,3	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1048696	1.00[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs10501375	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10501376	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10896957	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229868	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11229869	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11229870	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11229872	0.87[EUR][1000 genomes]
rs11229873	0.87[EUR][1000 genomes]
rs11229874	0.87[EUR][1000 genomes]
rs11229875	0.87[EUR][1000 genomes]
rs11229882	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11229889	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs11229901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs11229903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12223401	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12575770	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12576150	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12576412	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12576558	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12576879	0.87[EUR][1000 genomes]
rs12577252	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17153538	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1938595	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35654554	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3740946	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs3781796	0.87[EUR][1000 genomes]
rs59466005	0.87[EUR][1000 genomes]
rs60265864	0.87[EUR][1000 genomes]
rs61086875	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7104296	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7104437	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7926933	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7942203	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs869155	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv3351601	chr11:58979308-59052763	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv3381199	chr11:59015574-59068938	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv3407952	chr11:59029926-59032724	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11229904	DTX4	Cis_1M	lymphoblastoid	RTeQTL
rs11229904	MPEG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59028200-59034000	Weak transcription	GM12878-XiMat	blood
2	chr11:59029800-59039000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr11:59029800-59040400	Enhancers	Primary B cells from cord blood	blood
4	chr11:59030000-59035400	Enhancers	Primary B cells from peripheral blood	blood
5	chr11:59031200-59035400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr11:59031400-59039000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:59031600-59032800	Weak transcription	Liver	Liver
8	chr11:59031600-59033800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:59031600-59035000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr11:59031800-59033000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr11:59031800-59036800	Enhancers	Placenta	Placenta
12	chr11:59032000-59032800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:59032000-59036200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:59032200-59034400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:59032200-59036000	Enhancers	HMEC	breast
16	chr11:59032200-59036200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:59032400-59033000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:59032400-59036000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr11:59032600-59039200	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links