Variant report

Variant	rs62579389
Chromosome Location	chr9:103189320-103189321
allele	A/G
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	E2F6	chr9:103189172-103189492	K562	blood:	n/a	chr9:103189411-103189422
2	RFX5	chr9:103188826-103189392	K562	blood:	n/a	n/a
3	MAX	chr9:103188564-103189602	HCT-116	colon:	n/a	chr9:103188955-103188964
4	TAF1	chr9:103188755-103189688	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr9:103188735-103190414	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr9:103188795-103189456	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr9:103189220-103189370	HRPEpiC	eye:	n/a	chr9:103189359-103189368
8	POLR2A	chr9:103188739-103189695	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr9:103189320-103189470	HA-sp	spinal cord:	n/a	chr9:103189359-103189368
10	POLR2A	chr9:103188753-103189442	PFSK-1	brain:	n/a	n/a
11	CTCF	chr9:103189309-103189502	A549	lung:	n/a	chr9:103189359-103189368
12	MYBL2	chr9:103188790-103189338	HepG2	liver:	n/a	n/a
13	POLR2A	chr9:103188818-103190157	MCF-7	breast:	n/a	n/a
14	CEBPD	chr9:103189102-103189484	HepG2	liver:	n/a	n/a
15	JUND	chr9:103188781-103190307	A549	lung:	n/a	chr9:103188954-103188966 chr9:103188956-103188964 chr9:103188955-103188965 chr9:103188955-103188965 chr9:103188954-103188965
16	CTCF	chr9:103189320-103189470	HCM	heart:	n/a	chr9:103189359-103189368
17	ZKSCAN1	chr9:103188900-103189555	Hela-S3	cervix:	n/a	n/a
18	ZBTB7A	chr9:103189041-103189547	K562	blood:	n/a	n/a
19	BRCA1	chr9:103189222-103189407	HepG2	liver:	n/a	n/a
20	EGR1	chr9:103189158-103189896	K562	blood:	n/a	chr9:103189534-103189548
21	MAZ	chr9:103188809-103190287	Hela-S3	cervix:	n/a	chr9:103188955-103188964
22	MXI1	chr9:103188017-103189727	SK-N-SH	brain:	n/a	n/a
23	MAX	chr9:103189010-103189531	H1-hESC	embryonic stem cell:	n/a	n/a
24	MXI1	chr9:103188739-103189651	HepG2	liver:	n/a	n/a
25	BHLHE40	chr9:103188917-103189625	GM12878	blood:	n/a	chr9:103189368-103189384
26	YY1	chr9:103188951-103189463	ECC-1	luminal epithelium:	n/a	chr9:103189368-103189382
27	CTCF	chr9:103189240-103189390	HUVEC	blood vessel:	n/a	chr9:103189359-103189368
28	POLR2A	chr9:103188402-103189449	PBDE	blood:	n/a	n/a
29	SIN3AK20	chr9:103189195-103189696	K562	blood:	n/a	n/a
30	IRF1	chr9:103188546-103189434	K562	blood:	n/a	chr9:103188955-103188964 chr9:103189386-103189395
31	ZBTB7A	chr9:103189185-103189471	HepG2	liver:	n/a	n/a
32	TBL1XR1	chr9:103188841-103189463	GM12878	blood:	n/a	n/a
33	MAZ	chr9:103189125-103190223	GM12878	blood:	n/a	n/a
34	PAX5	chr9:103189206-103189459	GM12892	blood:	n/a	n/a
35	SIX5	chr9:103189055-103189338	A549	lung:	n/a	n/a
36	POLR2A	chr9:103188563-103190189	K562	blood:	n/a	n/a
37	ZNF143	chr9:103189186-103190182	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr9:103189300-103189450	WERI-Rb-1	eye:	n/a	chr9:103189359-103189368
39	POLR2A	chr9:103188791-103189586	HL-60	blood:	n/a	n/a
40	POLR2A	chr9:103188391-103189378	U87	brain:	n/a	n/a
41	POLR2A	chr9:103188753-103189754	MCF-7	breast:	n/a	n/a
42	TCF7L2	chr9:103188745-103189664	HCT-116	colon:	n/a	chr9:103188956-103188965
43	JUN	chr9:103188772-103189718	K562	blood:	n/a	chr9:103188954-103188966 chr9:103188956-103188964 chr9:103188955-103188965 chr9:103188955-103188965
44	FOXP2	chr9:103189247-103189535	PFSK-1	brain:	n/a	n/a
45	FOSL2	chr9:103188602-103189380	A549	lung:	n/a	chr9:103188954-103188966 chr9:103188956-103188964 chr9:103188955-103188965 chr9:103188955-103188965
46	TCF12	chr9:103188530-103189539	A549	lung:	n/a	n/a
47	RCOR1	chr9:103188510-103190318	K562	blood:	n/a	n/a
48	ZNF143	chr9:103188761-103189415	K562	blood:	n/a	n/a
49	RAD21	chr9:103188837-103189368	Hela-S3	cervix:	n/a	n/a
50	EP300	chr9:103188618-103189490	K562	blood:	n/a	chr9:103189370-103189379 chr9:103188788-103188802

No.	Distal block	Cell Line	Cell type
1	chr16:88519591..88520195-chr9:103189245..103190084,2	HCT-116	colon:
2	chr9:103188255..103190992-chr9:103234182..103236159,2	MCF-7	breast:
3	chr9:102587074..102589303-chr9:103188855..103190578,2	MCF-7	breast:
4	chr12:56510216..56511089-chr9:103188467..103189444,2	Hela-S3	cervix:
5	chr11:62608651..62609649-chr9:103188677..103189695,4	Hela-S3	cervix:
6	chr6:3000150..3000654-chr9:103188910..103189655,2	Hela-S3	cervix:
7	chr9:103108916..103110922-chr9:103189088..103192439,3	MCF-7	breast:
8	chr9:103108891..103111879-chr9:103188016..103191736,3	K562	blood:
9	chr3:57678348..57678964-chr9:103188755..103189418,2	Hela-S3	cervix:
10	chr9:103113279..103116752-chr9:103187119..103190910,6	K562	blood:
11	chr9:103182521..103185122-chr9:103187370..103189359,3	K562	blood:
12	chr9:103187999..103190908-chr9:103233595..103236918,6	MCF-7	breast:
13	chr9:102581117..102583683-chr9:103188604..103191068,4	K562	blood:
14	chr9:103112743..103119519-chr9:103186928..103191502,9	MCF-7	breast:
15	chr9:103112020..103116853-chr9:103187928..103193300,12	MCF-7	breast:
16	chr9:103113751..103117482-chr9:103187755..103190910,6	K562	blood:

Variant related genes	Relation type
MSANTD3	TF binding region
ENSG00000241697	Chromatin interaction
ENSG00000119508	Chromatin interaction
ENSG00000136891	Chromatin interaction
ENSG00000241933	Chromatin interaction
ENSG00000179588	Chromatin interaction
ENSG00000237461	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000174839	Chromatin interaction
ENSG00000124588	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

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	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv614955	chr9:103181596-103261227	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv3443911	chr9:103188156-103191004	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	esv3369267	chr9:103188781-103190679	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 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	chr9:103188400-103189800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:103188400-103190200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:103188400-103190200	Active TSS	HepG2	liver
4	chr9:103188400-103190600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr9:103188400-103191000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:103188600-103189400	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr9:103188600-103190000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:103188600-103190200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr9:103188600-103190200	Active TSS	Fetal Intestine Small	intestine
10	chr9:103188600-103190200	Active TSS	Stomach Smooth Muscle	stomach
11	chr9:103188600-103190400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr9:103188600-103190400	Active TSS	Fetal Kidney	kidney
13	chr9:103188600-103190400	Active TSS	Thymus	Thymus
14	chr9:103188600-103190400	Active TSS	A549	lung
15	chr9:103188600-103190600	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr9:103188600-103190600	Active TSS	Fetal Brain Male	brain
17	chr9:103188600-103190800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:103188600-103190800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:103188600-103190800	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr9:103188600-103191000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:103188600-103191000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:103188800-103189400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr9:103188800-103189400	Flanking Bivalent TSS/Enh	Dnd41	blood
24	chr9:103188800-103189600	Transcr. at gene 5' and 3'	Right Atrium	heart
25	chr9:103188800-103189800	Active TSS	Colonic Mucosa	Colon
26	chr9:103188800-103190000	Active TSS	Left Ventricle	heart
27	chr9:103188800-103190200	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr9:103188800-103190200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:103188800-103190200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:103188800-103190200	Active TSS	Primary T cells from cord blood	blood
31	chr9:103188800-103190200	Active TSS	Brain Angular Gyrus	brain
32	chr9:103188800-103190200	Active TSS	Fetal Intestine Large	intestine
33	chr9:103188800-103190400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:103188800-103190400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr9:103188800-103190400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:103188800-103190400	Active TSS	Esophagus	oesophagus
37	chr9:103188800-103190400	Active TSS	Gastric	stomach
38	chr9:103188800-103190400	Active TSS	Lung	lung
39	chr9:103188800-103190400	Active TSS	Ovary	ovary
40	chr9:103188800-103190400	Active TSS	Pancreas	Pancrea
41	chr9:103188800-103190600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr9:103188800-103190600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr9:103188800-103190600	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr9:103188800-103190600	Active TSS	Psoas Muscle	Psoas
45	chr9:103188800-103190800	Active TSS	Aorta	Aorta
46	chr9:103188800-103190800	Active TSS	Right Ventricle	heart
47	chr9:103188800-103191000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:103188800-103191200	Active TSS	HSMMtube	muscle
49	chr9:103188800-103192800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr9:103189000-103189400	Flanking Active TSS	Primary B cells from cord blood	blood

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