Variant report

Variant	rs10895904
Chromosome Location	chr11:105970134-105970135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:105965185..105968014-chr11:105969595..105971364,2	K562	blood:
2	chr11:105947655..105949809-chr11:105969558..105972572,3	MCF-7	breast:
3	chr11:105939028..105941380-chr11:105969620..105972203,2	K562	blood:

Variant related genes	Relation type
ENSG00000149313	Chromatin interaction
ENSG00000182359	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10791780	0.90[CHB][hapmap]
rs10895899	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10895900	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap]
rs11226915	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11226920	0.85[CHB][hapmap]
rs11226922	0.83[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11226931	0.86[ASN][1000 genomes]
rs12365489	0.90[CHB][hapmap]
rs17105049	0.85[CHB][hapmap];0.92[CHD][hapmap]
rs1893174	0.90[CHB][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap]
rs1939798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1939799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1940772	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2155340	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2186731	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277278	0.81[ASN][1000 genomes]
rs3740869	0.80[CHB][hapmap]
rs4237618	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4440991	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4474407	0.90[CHB][hapmap]
rs4565867	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4754141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60606604	0.81[ASN][1000 genomes]
rs7108636	0.85[CHB][hapmap]
rs7130759	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7131047	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs754562	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap]
rs7554	0.90[CHB][hapmap]
rs766717	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap]
rs9651674	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs9943677	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048381	chr11:105945117-106561574	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10895904	MMP12	cis	cerebellum	SCAN
rs10895904	AASDHPPT	cis	multi-tissue	Pritchard
rs10895904	AASDHPPT	Cis_1M	lymphoblastoid	RTeQTL
rs10895904	KDELC2	cis	cerebellum	SCAN
rs10895904	AASDHPPT	cis	lymphoblastoid	seeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:105949000-105973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:105949200-105971600	Weak transcription	Esophagus	oesophagus
3	chr11:105950400-105971200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:105953400-105970600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:105957200-105971000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:105957200-105976600	Weak transcription	Pancreas	Pancrea
7	chr11:105957200-105976800	Weak transcription	Aorta	Aorta
8	chr11:105958600-105971800	Weak transcription	Hela-S3	cervix
9	chr11:105959200-105970400	Strong transcription	Dnd41	blood
10	chr11:105959400-105970200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr11:105959400-105970200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr11:105959800-105970200	Weak transcription	Small Intestine	intestine
13	chr11:105959800-105970400	Weak transcription	Fetal Brain Male	brain
14	chr11:105961000-105970800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr11:105961000-105970800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr11:105961200-105970200	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr11:105961200-105970400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:105961400-105970400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr11:105961400-105970400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr11:105961400-105971600	Strong transcription	HSMM	muscle
21	chr11:105961600-105970400	Strong transcription	Adipose Nuclei	Adipose
22	chr11:105961600-105970400	Strong transcription	Liver	Liver
23	chr11:105961800-105970200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr11:105961800-105970400	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr11:105961800-105970600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr11:105962000-105970400	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr11:105962200-105970400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:105962200-105970400	Strong transcription	Primary B cells from cord blood	blood
29	chr11:105962400-105970600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:105963000-105972400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr11:105963200-105971800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr11:105963200-105972200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:105963400-105971400	Weak transcription	Thymus	Thymus
34	chr11:105964000-105971600	Weak transcription	Right Ventricle	heart
35	chr11:105964000-105971800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:105964200-105972000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr11:105965200-105970800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:105965200-105971200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr11:105965400-105970200	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr11:105966200-105970200	Strong transcription	HMEC	breast
41	chr11:105966800-105971600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr11:105966800-105971600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr11:105966800-105971800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:105966800-105972400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr11:105967000-105970600	Weak transcription	K562	blood
46	chr11:105967400-105971800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr11:105968400-105971200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr11:105968400-105971800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr11:105968400-105972200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:105968400-105972800	Weak transcription	Brain Angular Gyrus	brain

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