Variant report

Variant	rs7943857
Chromosome Location	chr11:74155120-74155121
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74153484..74156082-chr11:74157168..74159879,2	K562	blood:
2	chr11:73979603..73981610-chr11:74153903..74155501,2	MCF-7	breast:
3	chr11:74100543..74103930-chr11:74153911..74157152,3	MCF-7	breast:
4	chr11:74153867..74156607-chr11:74157168..74160666,3	K562	blood:
5	chr11:74108600..74111383-chr11:74152439..74157109,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264402	Chromatin interaction
ENSG00000165434	Chromatin interaction
ENSG00000149380	Chromatin interaction
ENSG00000254631	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11824535	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11826334	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12789112	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790352	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12798013	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12800641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35422358	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3867273	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3867275	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3913182	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4363632	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs66570137	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66959329	0.81[ASN][1000 genomes]
rs7129575	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv555443	chr11:74109166-74180489	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1041154	chr11:74114801-74177909	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv393	chr11:74135862-74181417	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7943857	KCTD14	cis	cerebellum	SCAN
rs7943857	XRRA1	cis	cerebellum	SCAN
rs7943857	ATG16L2	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74138800-74161600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:74152400-74156200	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr11:74152600-74155600	Enhancers	Fetal Intestine Large	intestine
4	chr11:74153200-74155800	Enhancers	Fetal Intestine Small	intestine
5	chr11:74153400-74155200	Enhancers	A549	lung
6	chr11:74153400-74155600	Enhancers	Duodenum Mucosa	Duodenum
7	chr11:74153400-74155600	Enhancers	Stomach Mucosa	stomach
8	chr11:74153400-74155600	Enhancers	K562	blood
9	chr11:74153400-74156800	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr11:74153600-74158400	Enhancers	Fetal Muscle Leg	muscle
11	chr11:74154000-74155200	Enhancers	Colonic Mucosa	Colon
12	chr11:74154000-74155800	Enhancers	HSMM	muscle
13	chr11:74154200-74155200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:74154200-74155800	Enhancers	HSMMtube	muscle
15	chr11:74154200-74156600	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr11:74154400-74155400	Weak transcription	Pancreas	Pancrea
17	chr11:74154400-74155600	Weak transcription	Psoas Muscle	Psoas
18	chr11:74154400-74160200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:74154400-74167600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:74154600-74155400	Weak transcription	Colon Smooth Muscle	Colon
21	chr11:74154600-74155600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr11:74154600-74167400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr11:74154600-74167800	Weak transcription	Liver	Liver
24	chr11:74154800-74155200	Weak transcription	Fetal Thymus	thymus
25	chr11:74154800-74155200	Weak transcription	Small Intestine	intestine
26	chr11:74154800-74155600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr11:74154800-74156200	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr11:74154800-74156600	Weak transcription	Osteobl	bone
29	chr11:74154800-74158800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr11:74154800-74160200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr11:74154800-74160200	Weak transcription	Hela-S3	cervix
32	chr11:74154800-74171600	Weak transcription	Fetal Kidney	kidney
33	chr11:74155000-74155200	Enhancers	Right Atrium	heart
34	chr11:74155000-74155600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr11:74155000-74156200	Enhancers	Ovary	ovary
36	chr11:74155000-74167400	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links