Variant report

Variant	rs1893498
Chromosome Location	chr11:102055452-102055453
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:102055332-102055536	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr11:102055440-102055590	HepG2	liver:	n/a	n/a
3	POLR2A	chr11:102055423-102055862	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:102053883..102056011-chr11:102058357..102060167,2	K562	blood:
2	chr11:101981375..101984225-chr11:102053761..102055595,2	MCF-7	breast:

Variant related genes	Relation type
YAP1	TF binding region
ENSG00000137693	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10895272	0.91[CEU][hapmap];0.86[CHB][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs10895273	0.87[EUR][1000 genomes]
rs10895274	0.87[EUR][1000 genomes]
rs10895275	0.87[EUR][1000 genomes]
rs10895276	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs10895277	0.91[CEU][hapmap];0.86[CHB][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs10895278	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs11225156	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11225160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11225163	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11225165	0.87[EUR][1000 genomes]
rs11225167	0.88[EUR][1000 genomes]
rs11225170	0.86[CEU][hapmap];0.86[CHB][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs11225174	0.91[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes]
rs11605954	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11608234	0.82[EUR][1000 genomes]
rs12223991	0.84[EUR][1000 genomes]
rs12226331	1.00[CEU][hapmap];0.92[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs12420287	0.96[EUR][1000 genomes]
rs12421242	0.94[EUR][1000 genomes]
rs12786272	0.88[EUR][1000 genomes]
rs12787996	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12790399	0.85[EUR][1000 genomes]
rs12793501	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12795624	1.00[CEU][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes]
rs17097547	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs17097560	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs1820455	0.88[EUR][1000 genomes]
rs1942683	0.82[ASW][hapmap];0.85[LWK][hapmap];0.80[MEX][hapmap];0.94[YRI][hapmap]
rs2187525	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282652	0.91[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs3858420	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs4420227	0.80[MEX][hapmap]
rs4447144	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4475891	0.91[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4561174	0.80[MEX][hapmap]
rs4754041	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4754833	0.87[GIH][hapmap]
rs57027482	0.82[EUR][1000 genomes]
rs58751289	0.84[EUR][1000 genomes]
rs7110557	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7120067	0.91[ASW][hapmap];0.95[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes]
rs7122907	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs7124247	0.84[EUR][1000 genomes]
rs7931576	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs7942061	0.88[EUR][1000 genomes]
rs8504	0.91[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs948737	0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3362945	chr11:101736547-102114246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv898333	chr11:101832670-102079986	Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1052348	chr11:101987090-102255753	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv556141	chr11:101988061-102207851	Weak transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1050961	chr11:101993880-102253717	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1051735	chr11:101993880-102255753	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv530646	chr11:102000840-102238992	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv832251	chr11:102012295-102181744	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1043388	chr11:102017719-102172857	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1893498	CASP1	cis	parietal	SCAN
rs1893498	C11orf70	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102026400-102059400	Weak transcription	Fetal Brain Male	brain
2	chr11:102028000-102062800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr11:102029200-102067600	Weak transcription	HSMMtube	muscle
4	chr11:102033400-102061000	Weak transcription	Right Ventricle	heart
5	chr11:102034400-102057200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr11:102034600-102076800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr11:102035400-102055600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr11:102036000-102069400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:102039600-102056800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:102041600-102062400	Weak transcription	Left Ventricle	heart
11	chr11:102042800-102057200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:102043800-102077000	Weak transcription	Esophagus	oesophagus
13	chr11:102043800-102100400	Weak transcription	Pancreas	Pancrea
14	chr11:102046600-102056800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:102046600-102057000	Weak transcription	Fetal Kidney	kidney
16	chr11:102046800-102056800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr11:102046800-102076600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr11:102047000-102057200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:102048200-102062400	Weak transcription	Liver	Liver
20	chr11:102048400-102065200	Weak transcription	Aorta	Aorta
21	chr11:102048400-102073600	Weak transcription	Psoas Muscle	Psoas
22	chr11:102048400-102077200	Weak transcription	Lung	lung
23	chr11:102049200-102056800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr11:102049200-102056800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr11:102049600-102055800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr11:102049600-102057000	Weak transcription	NH-A	brain
27	chr11:102049600-102057800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr11:102050000-102057200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr11:102050000-102057600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr11:102050200-102061600	Weak transcription	Small Intestine	intestine
31	chr11:102050400-102055600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:102050400-102076600	Weak transcription	Placenta	Placenta
33	chr11:102050600-102056800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr11:102050800-102057400	Weak transcription	A549	lung
35	chr11:102051000-102057200	Weak transcription	NHEK	skin
36	chr11:102051400-102076600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr11:102051800-102055600	Weak transcription	Fetal Stomach	stomach
38	chr11:102051800-102056600	Weak transcription	Hela-S3	cervix
39	chr11:102051800-102057000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr11:102052000-102062400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:102052000-102076600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:102052400-102057200	Weak transcription	Fetal Intestine Small	intestine
43	chr11:102053200-102055800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:102054200-102056200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:102054200-102059600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:102054400-102056600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr11:102054400-102057000	Weak transcription	Fetal Intestine Large	intestine
48	chr11:102054400-102058400	Enhancers	NHDF-Ad	bronchial
49	chr11:102054800-102055800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:102054800-102057000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links