Variant report

Variant	rs10896647
Chromosome Location	chr11:57571883-57571884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:57571832-57572221	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:57568699..57575383-chr11:57575572..57580605,8	K562	blood:
2	chr11:57570082..57573080-chr11:57578840..57580964,2	MCF-7	breast:
3	chr11:57529860..57532516-chr11:57571775..57573365,2	K562	blood:
4	chr11:57527671..57530404-chr11:57570684..57574039,3	MCF-7	breast:

Variant related genes	Relation type
CTNND1	TF binding region
ENSG00000198561	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10792112	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10896633	0.88[ASN][1000 genomes]
rs10896636	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11229113	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11229116	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11229130	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229131	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229148	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11570190	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11601320	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11601449	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11602109	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11604325	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11604333	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11605731	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11606396	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11607056	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12146541	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12362166	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12785533	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12790196	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12804972	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12805841	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12807250	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12807357	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1647405	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17455520	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2509808	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2847308	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2926656	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35808061	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3781885	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4827	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs488769	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs499188	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs527528	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs543725	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs547891	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs576859	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs589914	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs644883	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6591434	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs674094	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs682503	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs685149	0.82[ASN][1000 genomes]
rs708228	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7116341	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7117205	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7117878	0.84[ASN][1000 genomes]
rs7121169	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7129727	0.84[EUR][1000 genomes]
rs71484461	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71484468	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7932091	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7936998	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7938083	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7949841	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9420	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10896647	MED19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57556400-57587800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:57564400-57575600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:57567200-57573600	Weak transcription	Right Atrium	heart
4	chr11:57568200-57585800	Strong transcription	Fetal Muscle Trunk	muscle
5	chr11:57568200-57586000	Strong transcription	Fetal Muscle Leg	muscle
6	chr11:57568200-57588200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:57568400-57586600	Strong transcription	Placenta	Placenta
8	chr11:57568600-57581000	Strong transcription	K562	blood
9	chr11:57568600-57585800	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:57568600-57586000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr11:57568600-57586000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr11:57568600-57586400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr11:57568600-57586600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr11:57568600-57587000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr11:57568600-57587200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:57568600-57589000	Strong transcription	NHLF	lung
17	chr11:57568800-57575600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr11:57568800-57575600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr11:57568800-57585200	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr11:57568800-57585600	Strong transcription	Fetal Intestine Large	intestine
21	chr11:57568800-57589000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:57568800-57589000	Strong transcription	NH-A	brain
23	chr11:57569000-57573200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:57569000-57575200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:57569000-57575400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr11:57569000-57579000	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr11:57569000-57579200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
28	chr11:57569000-57580600	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr11:57569000-57583800	Strong transcription	NHDF-Ad	bronchial
30	chr11:57569000-57584800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
31	chr11:57569000-57584800	Strong transcription	HMEC	breast
32	chr11:57569000-57585000	Strong transcription	HepG2	liver
33	chr11:57569000-57585800	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr11:57569000-57586000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:57569000-57586400	Strong transcription	Brain Germinal Matrix	brain
36	chr11:57569000-57587000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:57569000-57587000	Strong transcription	NHEK	skin
38	chr11:57569000-57587200	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr11:57569000-57587400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:57569000-57587800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr11:57569000-57588800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:57569000-57589200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr11:57569200-57572400	Strong transcription	Colonic Mucosa	Colon
44	chr11:57569200-57574400	Strong transcription	Thymus	Thymus
45	chr11:57569200-57574600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr11:57569200-57577000	Strong transcription	Primary hematopoietic stem cells	blood
47	chr11:57569200-57577000	Strong transcription	Fetal Lung	lung
48	chr11:57569200-57579200	Strong transcription	Brain Cingulate Gyrus	brain
49	chr11:57569200-57579200	Strong transcription	Fetal Thymus	thymus
50	chr11:57569200-57579600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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