Variant report

Variant	rs9784962
Chromosome Location	chr7:25299501-25299502
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	CTCF	chr7:25299380-25299530	GM12872	blood:	n/a	chr7:25299446-25299459
2	FOS	chr7:25299398-25299566	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr7:25299380-25299530	SAEC	small airway:	n/a	chr7:25299446-25299459
4	CTCF	chr7:25299342-25299620	A549	lung:	n/a	chr7:25299446-25299459
5	MAX	chr7:25299341-25299565	H1-hESC	embryonic stem cell:	n/a	chr7:25299445-25299455 chr7:25299445-25299454 chr7:25299447-25299456
6	ZNF143	chr7:25299314-25299608	K562	blood:	n/a	n/a
7	CTCF	chr7:25299203-25299675	ECC-1	luminal epithelium:	n/a	chr7:25299446-25299459
8	CTCF	chr7:25299293-25299600	A549	lung:	n/a	chr7:25299446-25299459
9	CTCF	chr7:25299380-25299530	AoAF	blood vessel:	n/a	chr7:25299446-25299459
10	CTCF	chr7:25299360-25299510	HMEC	breast:	n/a	chr7:25299446-25299459
11	CTCF	chr7:25299318-25299560	MCF-7	breast:	n/a	chr7:25299446-25299459
12	CTCF	chr7:25299360-25299510	GM06990	blood:	n/a	chr7:25299446-25299459
13	CTCF	chr7:25299360-25299510	MCF-7	breast:	n/a	chr7:25299446-25299459
14	CTCF	chr7:25299299-25299582	Pancreas_OC	pancreas:	n/a	chr7:25299446-25299459
15	CTCF	chr7:25299318-25299586	ProgFib	skin:	n/a	chr7:25299446-25299459
16	CTCF	chr7:25299360-25299510	BE2_C	brain:	n/a	chr7:25299446-25299459
17	GTF2F1	chr7:25299361-25299579	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr7:25298613-25300359	SK-N-SH	brain:	n/a	chr7:25300049-25300057 chr7:25299446-25299459 chr7:25298949-25298959
19	CTCF	chr7:25299309-25299535	K562	blood:	n/a	chr7:25299446-25299459
20	CTCF	chr7:25299191-25299656	K562	blood:	n/a	chr7:25299446-25299459
21	CTCF	chr7:25299360-25299510	GM12875	blood:	n/a	chr7:25299446-25299459
22	CTCF	chr7:25299380-25299530	GM12867	blood:	n/a	chr7:25299446-25299459
23	CTCF	chr7:25299298-25299598	Medullo	brain:	n/a	chr7:25299446-25299459
24	ZNF143	chr7:25299298-25299648	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr7:25299360-25299510	HRE	kidney:	n/a	chr7:25299446-25299459
26	CTCF	chr7:25299360-25299510	Caco-2	colon:	n/a	chr7:25299446-25299459
27	SMC3	chr7:25299257-25299639	HepG2	liver:	n/a	n/a
28	RAD21	chr7:25298894-25300248	SK-N-SH	brain:	n/a	chr7:25298948-25298958
29	WRNIP1	chr7:25299232-25299654	GM12878	blood:	n/a	n/a
30	CTCF	chr7:25299400-25299550	GM12865	blood:	n/a	chr7:25299446-25299459
31	CTCF	chr7:25299400-25299550	GM12869	blood:	n/a	chr7:25299446-25299459
32	YY1	chr7:25299310-25299578	GM12878	blood:	n/a	n/a
33	CTCF	chr7:25299291-25299570	GM19239	blood:	n/a	chr7:25299446-25299459
34	CTCF	chr7:25299218-25299671	IMR90	lung:	n/a	chr7:25299446-25299459
35	MYC	chr7:25299268-25299673	NB4	blood:	n/a	chr7:25299445-25299455 chr7:25299445-25299454 chr7:25299447-25299456
36	RAD21	chr7:25299196-25299709	A549	lung:	n/a	n/a
37	CTCF	chr7:25299380-25299530	HBMEC	blood vessel:	n/a	chr7:25299446-25299459
38	CTCF	chr7:25299360-25299510	AG04449	skin:	n/a	chr7:25299446-25299459
39	CTCF	chr7:25299380-25299530	GM12868	blood:	n/a	chr7:25299446-25299459
40	RAD21	chr7:25299226-25299727	SK-N-SH_RA	brain:	n/a	n/a
41	RAD21	chr7:25299179-25299838	MCF-7	breast:	n/a	n/a
42	CTCF	chr7:25299380-25299530	NHLF	lung:	n/a	chr7:25299446-25299459
43	FOXA1	chr7:25299315-25299532	T-47D	breast:	n/a	n/a
44	CTCF	chr7:25299150-25299744	MCF-7	breast:	n/a	chr7:25299446-25299459
45	CTCF	chr7:25299229-25299645	HepG2	liver:	n/a	chr7:25299446-25299459
46	CTCF	chr7:25299380-25299530	HepG2	liver:	n/a	chr7:25299446-25299459
47	USF1	chr7:25299325-25299582	SK-N-SH_RA	brain:	n/a	n/a
48	CTCF	chr7:25299400-25299550	HFF	foreskin:	n/a	chr7:25299446-25299459
49	ZNF143	chr7:25299302-25299575	Hela-S3	cervix:	n/a	n/a
50	MAX	chr7:25299248-25299639	NB4	blood:	n/a	chr7:25299445-25299455 chr7:25299445-25299454 chr7:25299447-25299456

No.	Distal block	Cell Line	Cell type
1	chr7:25299370..25299906-chr7:25425808..25426760,2	MCF-7	breast:
2	chr7:25299400..25299900-chr7:25353345..25353911,2	MCF-7	breast:
3	chr7:25298959..25300333-chr7:25428102..25430106,21	MCF-7	breast:
4	chr7:25298951..25300126-chr7:25605192..25606795,18	K562	blood:
5	chr7:25298962..25299912-chr7:25428816..25430030,4	K562	blood:
6	chr7:25298470..25299852-chr7:25605228..25606576,11	MCF-7	breast:
7	chr7:25298973..25299854-chr7:25605283..25606167,4	MCF-7	breast:
8	chr7:25299070..25299853-chr7:25429198..25430452,5	MCF-7	breast:
9	chr7:25299061..25300348-chr7:25608226..25609143,4	K562	blood:

Variant related genes	Relation type
ENSG00000202233	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1008929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11770584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11770932	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11773410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12530684	1.00[ASN][1000 genomes]
rs12538631	1.00[ASN][1000 genomes]
rs13223273	1.00[ASN][1000 genomes]
rs17304305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2391107	1.00[ASN][1000 genomes]
rs34537571	1.00[ASN][1000 genomes]
rs6946398	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6961642	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs73092102	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv606424	chr7:24982529-25466521	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv606426	chr7:25254125-25621579	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25295200-25301000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:25295800-25301000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr7:25296000-25299600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:25296200-25300800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:25296600-25300400	Weak transcription	Fetal Brain Female	brain
6	chr7:25298800-25302200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:25299000-25302000	Enhancers	Colon Smooth Muscle	Colon
8	chr7:25299200-25299600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
9	chr7:25299200-25299600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
10	chr7:25299200-25299600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr7:25299200-25299600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr7:25299200-25299600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:25299200-25299600	Enhancers	Liver	Liver
14	chr7:25299200-25299600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
15	chr7:25299200-25299600	Enhancers	Fetal Intestine Small	intestine
16	chr7:25299200-25299600	Enhancers	Ovary	ovary
17	chr7:25299200-25299800	Enhancers	Fetal Brain Male	brain
18	chr7:25299200-25299800	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr7:25299200-25299800	Bivalent Enhancer	Dnd41	blood
20	chr7:25299200-25300000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:25299200-25300000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr7:25299200-25300000	Enhancers	Brain Substantia Nigra	brain
23	chr7:25299200-25300000	Enhancers	Fetal Intestine Large	intestine
24	chr7:25299200-25300000	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr7:25299200-25300000	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr7:25299200-25300000	Enhancers	NHEK	skin
27	chr7:25299200-25300200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr7:25299200-25300200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:25299200-25300200	Enhancers	Fetal Heart	heart
30	chr7:25299200-25300400	Enhancers	Brain Germinal Matrix	brain
31	chr7:25299200-25300600	Enhancers	Primary T cells fromperipheralblood	blood
32	chr7:25299200-25300600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr7:25299200-25300600	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr7:25299200-25300600	Enhancers	Duodenum Mucosa	Duodenum
35	chr7:25299200-25300600	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr7:25299200-25300800	Enhancers	Fetal Muscle Leg	muscle
37	chr7:25299200-25300800	Enhancers	Rectal Smooth Muscle	rectum
38	chr7:25299200-25300800	Enhancers	Thymus	Thymus
39	chr7:25299200-25301000	Enhancers	Brain Hippocampus Middle	brain
40	chr7:25299200-25301400	Enhancers	Fetal Kidney	kidney
41	chr7:25299200-25301600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr7:25299200-25301600	Enhancers	Fetal Lung	lung
43	chr7:25299200-25302200	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr7:25299200-25303800	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr7:25299400-25299600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr7:25299400-25299600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr7:25299400-25299600	Enhancers	Fetal Muscle Trunk	muscle
48	chr7:25299400-25299800	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr7:25299400-25299800	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr7:25299400-25299800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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