Variant report

Variant	rs10511963
Chromosome Location	chr9:71421359-71421360
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:73160073..73160620-chr9:71420702..71421682,2	NB4	blood:
2	chr3:73158387..73161479-chr9:71419682..71422682,3	K562	blood:
3	chr3:73160048..73160628-chr9:71420682..71421702,10	HCT-116	colon:
4	chr3:73159867..73160571-chr9:71420682..71421682,2	Hela-S3	cervix:
5	chr9:71420662..71423189-chr9:71425741..71428511,3	K562	blood:
6	chr9:71398048..71400496-chr9:71420484..71423422,2	K562	blood:
7	chr17:41398972..41401127-chr9:71419682..71422702,5	K562	blood:

Variant related genes	Relation type
ENSG00000223247	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10511962	0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs10781227	0.83[AMR][1000 genomes]
rs10781257	0.90[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap]
rs10869360	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10869365	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10869395	0.82[CEU][hapmap]
rs10869396	0.83[CEU][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10869400	0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs10869401	0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs10869403	0.83[CEU][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes]
rs10869407	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10869419	0.87[MEX][hapmap];0.88[AMR][1000 genomes]
rs11792022	0.83[AMR][1000 genomes]
rs1414944	0.83[MEX][hapmap]
rs2027025	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4504703	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs4745237	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4745268	0.86[EUR][1000 genomes]
rs4745295	0.95[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6560391	0.83[AMR][1000 genomes]
rs6560392	0.83[AMR][1000 genomes]
rs7031640	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7033278	0.91[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7035163	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs7856247	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7857352	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7864097	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs7874714	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs944856	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs952589	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs9776840	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv1050741	chr9:71405224-71450033	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv540148	chr9:71405224-71450033	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
13	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10511963	TJP2	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71404600-71431400	Weak transcription	HepG2	liver
2	chr9:71410200-71428600	Weak transcription	Aorta	Aorta
3	chr9:71414000-71437000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr9:71414000-71445000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:71416600-71422000	Enhancers	Primary B cells from peripheral blood	blood
6	chr9:71417400-71421800	Enhancers	Right Ventricle	heart
7	chr9:71417400-71423600	Enhancers	Left Ventricle	heart
8	chr9:71418600-71421400	Weak transcription	Colonic Mucosa	Colon
9	chr9:71418600-71444800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:71419600-71421800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr9:71419600-71422200	Genic enhancers	Primary B cells from cord blood	blood
12	chr9:71419800-71421600	Enhancers	Gastric	stomach
13	chr9:71419800-71421800	Enhancers	Fetal Muscle Leg	muscle
14	chr9:71419800-71421800	Enhancers	Pancreas	Pancrea
15	chr9:71419800-71422200	Enhancers	Rectal Smooth Muscle	rectum
16	chr9:71420000-71421400	Enhancers	Lung	lung
17	chr9:71420000-71421600	Enhancers	Right Atrium	heart
18	chr9:71420200-71421600	Enhancers	K562	blood
19	chr9:71420200-71422600	Enhancers	Fetal Stomach	stomach
20	chr9:71420400-71421800	Genic enhancers	Fetal Intestine Large	intestine
21	chr9:71420600-71421400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr9:71420600-71421400	Strong transcription	Duodenum Mucosa	Duodenum
23	chr9:71420600-71421400	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr9:71420600-71422600	Enhancers	GM12878-XiMat	blood
25	chr9:71420800-71421400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:71420800-71421400	Enhancers	Fetal Kidney	kidney
27	chr9:71420800-71421400	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr9:71420800-71422800	Enhancers	Colon Smooth Muscle	Colon
29	chr9:71420800-71424200	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr9:71420800-71434600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr9:71421000-71421400	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr9:71421000-71421600	Enhancers	Placenta	Placenta
33	chr9:71421000-71422200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:71421000-71424600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:71421000-71431800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr9:71421000-71437600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:71421200-71421400	Flanking Active TSS	Fetal Heart	heart
38	chr9:71421200-71421800	Strong transcription	Fetal Intestine Small	intestine
39	chr9:71421200-71424000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:71421200-71426000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:71421200-71437200	Weak transcription	Stomach Mucosa	stomach
42	chr9:71421200-71437600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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