Variant report

Variant	rs12420964
Chromosome Location	chr11:8811616-8811617
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	chr11:8806228..8807988-chr11:8810413..8812334,2	K562	blood:

Variant related genes	Relation type
ENSG00000255159	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10743086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10743087	0.83[LWK][hapmap]
rs10743089	0.83[LWK][hapmap]
rs10743090	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10769961	0.83[CEU][hapmap]
rs10840119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10840120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840122	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840124	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11042052	0.89[CEU][hapmap];0.80[CHB][hapmap]
rs11042064	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042073	0.82[EUR][1000 genomes]
rs11042074	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12269980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs12287694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12289240	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12291552	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16906037	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2316863	0.83[CEU][hapmap]
rs2873297	0.88[LWK][hapmap];0.87[YRI][hapmap]
rs3763917	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3763919	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3913547	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4082668	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4370937	0.88[CEU][hapmap]
rs4929918	0.83[CEU][hapmap]
rs55902154	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60869409	0.94[EUR][1000 genomes]
rs61875931	0.80[EUR][1000 genomes]
rs6484007	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6484606	0.88[CEU][hapmap]
rs7105372	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs7131166	0.88[CEU][hapmap];0.81[CHD][hapmap]
rs72858278	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7935617	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv553447	chr11:8792622-8825966	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12420964	DNHD1	cis	cerebellum	SCAN
rs12420964	RPL27A	cis	cerebellum	SCAN
rs12420964	MRVI1	cis	parietal	SCAN
rs12420964	PPFIBP2	cis	parietal	SCAN
rs12420964	OR51M1	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8797800-8827200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:8800800-8822400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:8800800-8825800	Weak transcription	Brain Angular Gyrus	brain
4	chr11:8800800-8827400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:8801000-8815600	Weak transcription	NHDF-Ad	bronchial
6	chr11:8801600-8820000	Weak transcription	HSMMtube	muscle
7	chr11:8801600-8827400	Weak transcription	Esophagus	oesophagus
8	chr11:8801800-8814200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:8802000-8816000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr11:8802200-8819200	Weak transcription	NH-A	brain
11	chr11:8802800-8816000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr11:8803000-8815800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:8803000-8820600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:8807000-8811800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr11:8807600-8814000	Weak transcription	Fetal Lung	lung
16	chr11:8807600-8815200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr11:8807800-8814200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:8808200-8813200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr11:8808200-8815800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:8808400-8812000	Weak transcription	Fetal Intestine Small	intestine
21	chr11:8808600-8814400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:8808600-8819400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:8808800-8816000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr11:8808800-8816200	Weak transcription	Brain Hippocampus Middle	brain
25	chr11:8809000-8812400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:8809000-8813800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr11:8809000-8814000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:8809000-8815800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr11:8809000-8816000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr11:8809000-8816200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr11:8809000-8830200	Weak transcription	Fetal Brain Male	brain
32	chr11:8809200-8811800	Weak transcription	NHEK	skin
33	chr11:8809200-8813800	Weak transcription	HepG2	liver
34	chr11:8809200-8814200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr11:8809200-8814400	Weak transcription	Adipose Nuclei	Adipose
36	chr11:8809200-8815600	Weak transcription	HSMM	muscle
37	chr11:8809200-8815800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr11:8809200-8816200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr11:8809200-8826600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr11:8809200-8829200	Weak transcription	Fetal Kidney	kidney
41	chr11:8809400-8814200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:8809400-8814200	Weak transcription	Fetal Muscle Leg	muscle
43	chr11:8809400-8815800	Weak transcription	Placenta	Placenta
44	chr11:8809800-8812400	Strong transcription	Fetal Stomach	stomach
45	chr11:8810000-8812800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr11:8810000-8815800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr11:8810200-8812800	Enhancers	Small Intestine	intestine
48	chr11:8810400-8811800	Enhancers	Hela-S3	cervix
49	chr11:8810400-8812400	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr11:8810400-8815800	Weak transcription	Spleen	Spleen

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