Variant report

Variant	rs10821161
Chromosome Location	chr9:96338382-96338383
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	chr9:96338013-96338945	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr9:96337939-96339819	K562	blood:	n/a	n/a
3	POLR2A	chr9:96338026-96339300	Raji	blood:	n/a	n/a
4	ZMIZ1	chr9:96338128-96338560	K562	blood:	n/a	n/a
5	POLR2A	chr9:96338070-96338556	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr9:96337905-96338631	U87	brain:	n/a	n/a
7	POLR2A	chr9:96337911-96338631	U87	brain:	n/a	n/a
8	UBTF	chr9:96338001-96338809	K562	blood:	n/a	n/a
9	HEY1	chr9:96338055-96338397	K562	blood:	n/a	n/a
10	TAF1	chr9:96338137-96338470	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr9:96337940-96340262	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr9:96337579-96339836	GM18505	blood:	n/a	n/a
13	RUNX3	chr9:96337972-96338404	GM12878	blood:	n/a	n/a
14	POLR2A	chr9:96338099-96338458	HepG2	liver:	n/a	n/a
15	POLR2A	chr9:96338115-96338414	U87	brain:	n/a	n/a
16	POLR2A	chr9:96338060-96338430	PFSK-1	brain:	n/a	n/a
17	HCFC1	chr9:96338107-96338785	K562	blood:	n/a	n/a
18	POLR2A	chr9:96338081-96338506	K562	blood:	n/a	n/a
19	TBP	chr9:96338135-96338409	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr9:96337825-96340014	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr9:96337916-96339960	GM12892	blood:	n/a	n/a
22	POLR2A	chr9:96337483-96339925	K562	blood:	n/a	n/a
23	MTA3	chr9:96337986-96338431	GM12878	blood:	n/a	n/a
24	POLR2A	chr9:96337949-96338792	Hela-S3	cervix:	n/a	n/a
25	TBP	chr9:96338008-96339257	K562	blood:	n/a	n/a
26	GTF2B	chr9:96338179-96338431	K562	blood:	n/a	n/a
27	YY1	chr9:96337992-96339507	K562	blood:	n/a	chr9:96339333-96339347 chr9:96339339-96339348 chr9:96338199-96338213 chr9:96339459-96339473 chr9:96338851-96338865 chr9:96339051-96339063 chr9:96339360-96339374 chr9:96339370-96339384
28	POLR2A	chr9:96337960-96338672	SK-N-MC	brain:	n/a	n/a
29	ELF1	chr9:96337983-96338391	K562	blood:	n/a	chr9:96338152-96338165 chr9:96338153-96338164
30	MAZ	chr9:96337939-96339226	K562	blood:	n/a	chr9:96338698-96338708
31	UBTF	chr9:96337990-96340266	K562	blood:	n/a	n/a
32	POLR2A	chr9:96337865-96340314	MCF10A-Er-Src	breast:	n/a	n/a
33	TAF1	chr9:96338112-96338425	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr9:96338111-96339198	HepG2	liver:	n/a	n/a
35	MAZ	chr9:96338140-96339202	Hela-S3	cervix:	n/a	chr9:96338698-96338708
36	POLR2A	chr9:96338065-96339323	H1-neurons	neurons:	n/a	n/a
37	SPI1	chr9:96337638-96338429	GM12878	blood:	n/a	chr9:96338155-96338164 chr9:96338076-96338083 chr9:96338153-96338166 chr9:96338156-96338163 chr9:96338152-96338165 chr9:96338152-96338165
38	POLR2A	chr9:96338108-96338478	GM12878	blood:	n/a	n/a
39	CCNT2	chr9:96338204-96339839	K562	blood:	n/a	chr9:96339670-96339679
40	TAF1	chr9:96337894-96338931	K562	blood:	n/a	n/a
41	YY1	chr9:96338160-96338532	GM12878	blood:	n/a	chr9:96338199-96338213
42	TAF1	chr9:96337908-96339329	ECC-1	luminal epithelium:	n/a	n/a
43	REST	chr9:96337337-96340269	H1-neurons	neurons:	n/a	chr9:96339630-96339643 chr9:96339814-96339832 chr9:96338320-96338330
44	POLR2A	chr9:96337533-96339108	IMR90	lung:	n/a	n/a
45	MAZ	chr9:96337511-96340494	IMR90	lung:	n/a	chr9:96339336-96339346 chr9:96339537-96339547 chr9:96338698-96338708 chr9:96340026-96340036
46	TBP	chr9:96338040-96338488	GM12878	blood:	n/a	n/a
47	POLR2A	chr9:96337948-96338958	GM12878	blood:	n/a	n/a
48	ZC3H11A	chr9:96338164-96338428	K562	blood:	n/a	n/a
49	EP300	chr9:96338117-96338441	GM12878	blood:	n/a	chr9:96338155-96338164
50	POLR2A	chr9:96337909-96338917	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:101964530..101966057-chr9:96338377..96341052,2	MCF-7	breast:
2	chr9:96213158..96214882-chr9:96338001..96341678,3	K562	blood:
3	chr9:96211528..96214948-chr9:96337573..96343441,10	MCF-7	breast:
4	chr9:96211672..96218862-chr9:96335264..96341672,16	MCF-7	breast:
5	chr9:96337024..96339848-chr9:96617971..96619932,2	MCF-7	breast:
6	chr9:95895154..95898000-chr9:96338001..96340609,3	MCF-7	breast:
7	chr9:95856094..95858375-chr9:96337008..96340445,3	MCF-7	breast:
8	chr8:144819610..144821971-chr9:96337841..96340310,2	MCF-7	breast:
9	chr14:52455551..52457081-chr9:96338294..96340039,2	MCF-7	breast:
10	chr9:96337657..96339290-chr9:96927321..96930180,2	K562	blood:
11	chr9:95894803..95898160-chr9:96337820..96340366,3	MCF-7	breast:
12	chr9:96214499..96217099-chr9:96338317..96340265,2	K562	blood:

Variant related genes	Relation type
PHF2	TF binding region
ENSG00000231990	Chromatin interaction
ENSG00000223446	Chromatin interaction
ENSG00000188938	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000087302	Chromatin interaction
ENSG00000131669	Chromatin interaction
ENSG00000269946	Chromatin interaction
ENSG00000203499	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10821156	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10821183	1.00[MEX][hapmap]
rs2254351	1.00[CEU][hapmap]
rs4330749	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4743925	1.00[CEU][hapmap]
rs4743926	1.00[CEU][hapmap]
rs4744241	1.00[YRI][hapmap]
rs4744244	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs6479489	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs6479490	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs6479491	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7021710	0.88[CEU][hapmap]
rs928367	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9409478	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041803	chr9:96299639-96342013	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv824985	chr9:96337735-96340349	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	esv3359621	chr9:96337881-96340629	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	esv3422729	chr9:96337956-96340504	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96337000-96338400	Enhancers	Fetal Heart	heart
2	chr9:96337200-96338400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:96337200-96338400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:96337200-96338400	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr9:96337400-96338400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr9:96337400-96338400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr9:96337400-96338400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr9:96337400-96338400	Flanking Active TSS	Fetal Muscle Trunk	muscle
9	chr9:96337400-96338400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr9:96337600-96338400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr9:96337600-96338400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr9:96337600-96338400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:96337600-96338400	Flanking Active TSS	Fetal Thymus	thymus
14	chr9:96337600-96339600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr9:96337600-96340000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:96337600-96340000	Active TSS	Ovary	ovary
17	chr9:96337600-96340000	Active TSS	A549	lung
18	chr9:96337600-96340200	Active TSS	Aorta	Aorta
19	chr9:96337600-96340400	Active TSS	H9 Cell Line	embryonic stem cell
20	chr9:96337600-96340400	Active TSS	Fetal Kidney	kidney
21	chr9:96337600-96340600	Active TSS	HSMMtube	muscle
22	chr9:96337600-96341000	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr9:96337800-96338400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:96337800-96338400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr9:96337800-96338400	Flanking Active TSS	Liver	Liver
26	chr9:96337800-96338400	Flanking Active TSS	K562	blood
27	chr9:96337800-96338600	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr9:96337800-96339800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:96337800-96339800	Active TSS	Right Atrium	heart
30	chr9:96337800-96339800	Active TSS	Osteobl	bone
31	chr9:96337800-96340000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr9:96337800-96340000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:96337800-96340000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:96337800-96340000	Active TSS	Colon Smooth Muscle	Colon
35	chr9:96337800-96340000	Active TSS	Fetal Lung	lung
36	chr9:96337800-96340000	Active TSS	HSMM	muscle
37	chr9:96337800-96340000	Active TSS	NHDF-Ad	bronchial
38	chr9:96337800-96340200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr9:96337800-96340200	Active TSS	Small Intestine	intestine
40	chr9:96337800-96340400	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr9:96338000-96338400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
42	chr9:96338000-96338400	Bivalent/Poised TSS	HepG2	liver
43	chr9:96338000-96338600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:96338000-96338600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr9:96338000-96338600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
46	chr9:96338000-96338600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr9:96338000-96338600	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr9:96338000-96338600	Active TSS	Placenta Amnion	Placenta Amnion
49	chr9:96338000-96338600	Active TSS	Stomach Mucosa	stomach
50	chr9:96338000-96338800	Active TSS	Primary T helper naive cells from peripheral blood	blood

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