Variant report

Variant	rs10896633
Chromosome Location	chr11:57424040-57424041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:57423998-57425889	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr11:57424029-57425405	A549	lung:	n/a	chr11:57425194-57425201 chr11:57425064-57425074
3	SREBP1	chr11:57423898-57425581	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57242576..57245304-chr11:57423792..57425526,2	MCF-7	breast:
2	chr11:57407680..57409367-chr11:57422916..57424875,2	MCF-7	breast:
3	chr11:57423095..57430151-chr11:57432283..57438412,24	K562	blood:
4	chr11:57423375..57427275-chr11:57433374..57437610,8	MCF-7	breast:
5	chr11:57423749..57426682-chr11:57508630..57510179,2	K562	blood:
6	chr11:57415734..57418167-chr11:57421184..57424253,3	K562	blood:
7	chr11:57423476..57425127-chr11:58344978..58347964,2	K562	blood:
8	chr11:57194115..57196219-chr11:57423627..57426056,2	K562	blood:
9	chr11:57411538..57415148-chr11:57422707..57424942,3	K562	blood:
10	chr11:57333149..57335001-chr11:57423752..57425633,2	MCF-7	breast:
11	chr11:57414343..57418921-chr11:57423216..57427343,7	K562	blood:

No data

Variant related genes	Relation type
CLP1	TF binding region
ENSG00000166793	Chromatin interaction
ENSG00000254602	Chromatin interaction
ENSG00000254732	Chromatin interaction
ENSG00000186660	Chromatin interaction
ENSG00000211450	Chromatin interaction
ENSG00000134802	Chromatin interaction
ENSG00000255073	Chromatin interaction
ENSG00000208009	Chromatin interaction
ENSG00000110031	Chromatin interaction
ENSG00000172409	Chromatin interaction
ENSG00000255301	Chromatin interaction
ENSG00000156599	Chromatin interaction
ENSG00000156587	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10792112	0.84[ASN][1000 genomes]
rs10896636	0.91[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10896647	0.88[ASN][1000 genomes]
rs11229066	1.00[JPT][hapmap]
rs11229067	1.00[ASW][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap]
rs11229075	0.83[AFR][1000 genomes]
rs11229113	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229116	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11229130	0.84[ASN][1000 genomes]
rs11229131	0.84[ASN][1000 genomes]
rs11229148	0.88[ASN][1000 genomes]
rs11570190	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11570195	0.90[LWK][hapmap]
rs11601320	0.81[ASN][1000 genomes]
rs11601449	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11602109	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11603020	1.00[ASW][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap]
rs11604325	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11604333	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11605731	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11606396	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11606677	1.00[JPT][hapmap]
rs11607056	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12146541	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12362166	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12785533	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12790196	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12804972	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12805841	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12807250	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs1647395	0.86[ASN][1000 genomes]
rs1647405	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17455520	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2081361	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2847308	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2926656	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35808061	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3824988	1.00[ASW][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap]
rs4827	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs488769	0.90[CEU][hapmap];0.89[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4926	1.00[JPT][hapmap]
rs499188	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs527528	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs543725	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs547891	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55649513	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55920079	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs576859	0.95[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs682503	0.81[ASN][1000 genomes]
rs708228	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs7116341	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7117205	0.81[ASN][1000 genomes]
rs7117878	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7121169	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7129727	0.80[EUR][1000 genomes]
rs71484461	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs731384	1.00[ASW][hapmap];0.81[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7932091	0.88[ASN][1000 genomes]
rs7938083	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7949841	0.91[ASN][1000 genomes]
rs9420	0.95[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10896633	OR4D10	cis	parietal	SCAN
rs10896633	OR5T1	cis	cerebellum	SCAN
rs10896633	MED19	cis	cerebellum	SCAN
rs10896633	PRG3	cis	parietal	SCAN
rs10896633	LRRC55	cis	parietal	SCAN
rs10896633	MS4A7	cis	parietal	SCAN
rs10896633	TIMM10	cis	parietal	SCAN
rs10896633	DDB1	cis	cerebellum	SCAN
rs10896633	MS4A7	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57417800-57424600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:57417800-57424600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:57418000-57424200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr11:57418000-57424200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr11:57418000-57424200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr11:57418000-57424200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:57418000-57424400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr11:57418000-57424600	Weak transcription	Right Atrium	heart
9	chr11:57418000-57424600	Weak transcription	HSMM	muscle
10	chr11:57418200-57424200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:57418200-57424200	Weak transcription	Brain Hippocampus Middle	brain
12	chr11:57418200-57424400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr11:57418400-57424600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:57418600-57424200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:57418600-57424600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:57418800-57424600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:57420200-57424200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr11:57420400-57424400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr11:57420400-57424400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:57420400-57424400	Weak transcription	Thymus	Thymus
21	chr11:57420600-57424200	Weak transcription	Primary T cells from cord blood	blood
22	chr11:57420600-57424200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:57420600-57424200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr11:57420600-57424400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr11:57420600-57424400	Weak transcription	NHLF	lung
26	chr11:57420800-57424200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:57420800-57424200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr11:57420800-57424200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr11:57420800-57424200	Weak transcription	Adipose Nuclei	Adipose
30	chr11:57420800-57424200	Weak transcription	K562	blood
31	chr11:57420800-57424400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:57420800-57424400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:57420800-57424400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr11:57420800-57424400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr11:57420800-57424400	Weak transcription	Osteobl	bone
36	chr11:57421000-57424200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:57421000-57424400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr11:57421400-57424200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr11:57421400-57424200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:57421400-57424200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:57421400-57424200	Weak transcription	Fetal Thymus	thymus
42	chr11:57421400-57424400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr11:57421400-57424400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:57421400-57424400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:57421400-57424400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr11:57421400-57424400	Weak transcription	Primary B cells from cord blood	blood
47	chr11:57421400-57424400	Weak transcription	Fetal Lung	lung
48	chr11:57421600-57424400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr11:57422000-57424400	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr11:57422200-57424200	Weak transcription	Placenta	Placenta

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