Variant report

Variant	rs10488704
Chromosome Location	chr11:32863470-32863471
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:32862183..32864294-chr11:32914218..32916079,2	K562	blood:
2	chr11:32862368..32865112-chr11:32868900..32870710,2	K562	blood:
3	chr11:32850866..32853799-chr11:32862127..32863701,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000060749	Chromatin interaction
ENSG00000135378	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10488703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767970	0.86[CHB][hapmap]
rs10767971	0.92[ASN][1000 genomes]
rs10767972	0.92[ASN][1000 genomes]
rs10835981	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10835983	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10835989	0.82[ASN][1000 genomes]
rs11031964	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs11032001	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11032024	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11032025	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs11032032	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11032033	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11032034	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11032044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11032046	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11032047	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11821224	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11826294	0.92[ASN][1000 genomes]
rs1556802	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs16923617	0.91[ASN][1000 genomes]
rs17251699	1.00[LWK][hapmap]
rs197705	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs197707	0.94[ASN][1000 genomes]
rs197710	0.93[ASN][1000 genomes]
rs201845	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs2024636	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap]
rs2664692	0.92[ASN][1000 genomes]
rs28449959	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2900981	0.84[ASN][1000 genomes]
rs4755454	0.84[ASN][1000 genomes]
rs4756329	0.87[CHB][hapmap]
rs55744018	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55763432	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56230223	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56695506	0.86[AFR][1000 genomes]
rs60475066	0.90[ASN][1000 genomes]
rs60529855	0.83[ASN][1000 genomes]
rs7108128	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs7118630	0.94[ASN][1000 genomes]
rs7122029	0.85[ASN][1000 genomes]
rs7122130	0.85[ASN][1000 genomes]
rs72899241	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72899242	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72901219	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72901225	0.91[ASN][1000 genomes]
rs72901227	0.91[ASN][1000 genomes]
rs7483614	1.00[YRI][hapmap]
rs7933966	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7943715	0.83[ASN][1000 genomes]
rs7944652	0.87[CHB][hapmap]
rs926735	1.00[ASW][hapmap]
rs956322	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9943603	0.92[ASN][1000 genomes]
rs9943661	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758262	chr11:32714643-33049940	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2759815	chr11:32714643-33049940	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	esv2757434	chr11:32792784-32958609	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv34742	chr11:32796092-33004024	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	esv2753057	chr11:32796124-33061724	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	esv2753743	chr11:32796124-33084924	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv897190	chr11:32801921-32951836	Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv897191	chr11:32805169-32903263	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv897192	chr11:32828760-32903263	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv897193	chr11:32838288-32903263	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10488704	C11orf41	cis	parietal	SCAN
rs10488704	ANXA2P1	trans	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:32852200-32876800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:32852800-32863800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:32852800-32871000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr11:32852800-32878800	Weak transcription	Placenta	Placenta
5	chr11:32853000-32877200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:32854000-32871200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr11:32855000-32876800	Weak transcription	Esophagus	oesophagus
8	chr11:32858600-32873800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr11:32860800-32864600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr11:32861000-32865400	Weak transcription	HMEC	breast
11	chr11:32861000-32865600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:32861000-32869200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr11:32861000-32872200	Weak transcription	Gastric	stomach
14	chr11:32861200-32873400	Weak transcription	NHEK	skin
15	chr11:32861600-32870800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:32862400-32864600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr11:32862400-32873600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr11:32862400-32873600	Weak transcription	Hela-S3	cervix
19	chr11:32862600-32865400	Weak transcription	Liver	Liver
20	chr11:32863200-32873800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr11:32863400-32867400	Weak transcription	Fetal Intestine Small	intestine
22	chr11:32863400-32867800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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