Variant report

Variant	rs2316863
Chromosome Location	chr11:8838828-8838829
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8835358..8837463-chr11:8838521..8841389,2	MCF-7	breast:
2	chr11:8707625..8713219-chr11:8836057..8840145,5	K562	blood:
3	chr11:8708284..8710316-chr11:8838549..8840292,2	MCF-7	breast:
4	chr11:8708066..8711768-chr11:8837087..8840258,4	MCF-7	breast:
5	chr11:8707625..8711209-chr11:8836057..8839950,3	K562	blood:

Variant related genes	Relation type
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10743086	0.82[CEU][hapmap]
rs10769961	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769965	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840119	0.82[CEU][hapmap]
rs10840120	0.83[CEU][hapmap];0.81[CHD][hapmap]
rs10840128	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs10840131	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840132	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11042064	0.83[CEU][hapmap]
rs11042085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042087	0.94[ASN][1000 genomes]
rs11042089	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12269980	0.83[CEU][hapmap];0.81[CHD][hapmap]
rs12287694	0.83[CEU][hapmap]
rs12419731	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12420964	0.83[CEU][hapmap]
rs13377459	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16906037	0.83[CEU][hapmap]
rs2568025	0.86[LWK][hapmap]
rs2568031	0.83[LWK][hapmap]
rs2568032	0.81[LWK][hapmap]
rs3763917	0.83[CEU][hapmap];0.84[CHD][hapmap]
rs3763919	0.81[CHD][hapmap]
rs3913547	0.83[CEU][hapmap];0.81[CHD][hapmap]
rs4082668	0.83[CEU][hapmap]
rs4244805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4370937	0.82[CEU][hapmap]
rs4929918	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4929919	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6484606	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7127564	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7131166	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7930737	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7930878	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7935617	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7947553	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[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	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv527920	chr11:8816695-8856822	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv527073	chr11:8829168-8848463	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2316863	CSNK2A1P	cis	cerebellum	SCAN
rs2316863	TUB	cis	parietal	SCAN
rs2316863	PPFIBP2	cis	parietal	SCAN
rs2316863	RPL27A	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8832600-8840800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:8833000-8839200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:8833200-8859800	Weak transcription	Aorta	Aorta
4	chr11:8834200-8839000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:8835600-8840000	Weak transcription	Colonic Mucosa	Colon
6	chr11:8835600-8845000	Weak transcription	Psoas Muscle	Psoas
7	chr11:8835600-8848800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr11:8835800-8840600	Weak transcription	Fetal Stomach	stomach
9	chr11:8836200-8843000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr11:8836200-8843600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr11:8836200-8844000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:8836200-8844200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr11:8836200-8848000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:8836400-8844000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:8836400-8847600	Weak transcription	Fetal Muscle Leg	muscle
16	chr11:8836400-8849800	Weak transcription	Fetal Intestine Small	intestine
17	chr11:8836600-8839800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:8836600-8850400	Weak transcription	Fetal Lung	lung
19	chr11:8836800-8840000	Weak transcription	Ovary	ovary
20	chr11:8836800-8847600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr11:8836800-8848600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr11:8837000-8850000	Weak transcription	Lung	lung
23	chr11:8837200-8843800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr11:8837200-8847000	Weak transcription	HSMMtube	muscle
25	chr11:8837200-8847200	Weak transcription	NHDF-Ad	bronchial
26	chr11:8837200-8847600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:8837200-8847600	Weak transcription	Fetal Kidney	kidney
28	chr11:8837200-8848000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:8837200-8848600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr11:8837400-8839800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr11:8837400-8839800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr11:8837400-8840000	Weak transcription	Placenta	Placenta
33	chr11:8837400-8843200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr11:8837400-8847000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:8837400-8847200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr11:8837400-8848000	Weak transcription	NHEK	skin
37	chr11:8837600-8843800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr11:8837600-8847200	Weak transcription	NHLF	lung
39	chr11:8837800-8848400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr11:8838000-8848400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr11:8838200-8843800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr11:8838600-8844800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:8838800-8839200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:8838800-8839200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr11:8838800-8839600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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