Variant report

Variant	rs1008929
Chromosome Location	chr7:25299726-25299727
allele	A/C/G/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	CTCF	chr7:25298613-25300359	SK-N-SH	brain:	n/a	chr7:25300049-25300057 chr7:25299446-25299459 chr7:25298949-25298959
2	RAD21	chr7:25298894-25300248	SK-N-SH	brain:	n/a	chr7:25298948-25298958
3	RAD21	chr7:25299226-25299727	SK-N-SH_RA	brain:	n/a	n/a
4	RAD21	chr7:25299179-25299838	MCF-7	breast:	n/a	n/a
5	CTCF	chr7:25299150-25299744	MCF-7	breast:	n/a	chr7:25299446-25299459
6	RAD21	chr7:25299168-25299812	HCT-116	colon:	n/a	n/a
7	RAD21	chr7:25299205-25299881	HCT-116	colon:	n/a	n/a
8	SMC3	chr7:25299233-25299765	GM12878	blood:	n/a	n/a
9	CTCF	chr7:25299138-25299887	HCT-116	colon:	n/a	chr7:25299446-25299459
10	CTCF	chr7:25299158-25299813	HCT-116	colon:	n/a	chr7:25299446-25299459
11	SMC3	chr7:25298626-25300186	SK-N-SH	brain:	n/a	chr7:25298951-25298959 chr7:25298948-25298958
12	RAD21	chr7:25299163-25299753	ECC-1	luminal epithelium:	n/a	n/a
13	CTCF	chr7:25299041-25299954	A549	lung:	n/a	chr7:25299446-25299459
14	RAD21	chr7:25299133-25299776	A549	lung:	n/a	n/a
15	CTCF	chr7:25299137-25299780	MCF-7	breast:	n/a	chr7:25299446-25299459

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	chr7:25299530..25302516-chr7:25303123..25304940,2	K562	blood:
10	chr7:25299061..25300348-chr7:25608226..25609143,4	K562	blood:

Variant related genes	Relation type
ENSG00000202233	TF binding region
ENSG00000202233	Chromatin interaction

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

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

rs_ID	r²[population]
rs11769704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[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];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11770932	0.84[AFR][1000 genomes];0.97[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];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12530684	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12538631	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13223273	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17304305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2391107	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34537571	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6946398	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6961642	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs73092102	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9784962	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]

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:62 , 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	chr7:25296200-25300800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:25296600-25300400	Weak transcription	Fetal Brain Female	brain
5	chr7:25298800-25302200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:25299000-25302000	Enhancers	Colon Smooth Muscle	Colon
7	chr7:25299200-25299800	Enhancers	Fetal Brain Male	brain
8	chr7:25299200-25299800	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr7:25299200-25299800	Bivalent Enhancer	Dnd41	blood
10	chr7:25299200-25300000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:25299200-25300000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr7:25299200-25300000	Enhancers	Brain Substantia Nigra	brain
13	chr7:25299200-25300000	Enhancers	Fetal Intestine Large	intestine
14	chr7:25299200-25300000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr7:25299200-25300000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr7:25299200-25300000	Enhancers	NHEK	skin
17	chr7:25299200-25300200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr7:25299200-25300200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr7:25299200-25300200	Enhancers	Fetal Heart	heart
20	chr7:25299200-25300400	Enhancers	Brain Germinal Matrix	brain
21	chr7:25299200-25300600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr7:25299200-25300600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr7:25299200-25300600	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr7:25299200-25300600	Enhancers	Duodenum Mucosa	Duodenum
25	chr7:25299200-25300600	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr7:25299200-25300800	Enhancers	Fetal Muscle Leg	muscle
27	chr7:25299200-25300800	Enhancers	Rectal Smooth Muscle	rectum
28	chr7:25299200-25300800	Enhancers	Thymus	Thymus
29	chr7:25299200-25301000	Enhancers	Brain Hippocampus Middle	brain
30	chr7:25299200-25301400	Enhancers	Fetal Kidney	kidney
31	chr7:25299200-25301600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr7:25299200-25301600	Enhancers	Fetal Lung	lung
33	chr7:25299200-25302200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr7:25299200-25303800	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr7:25299400-25299800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr7:25299400-25299800	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr7:25299400-25299800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr7:25299400-25299800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr7:25299400-25299800	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr7:25299400-25299800	Enhancers	NH-A	brain
41	chr7:25299400-25300000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr7:25299400-25300000	Enhancers	Osteobl	bone
43	chr7:25299400-25300200	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr7:25299400-25300200	Enhancers	Adipose Nuclei	Adipose
45	chr7:25299400-25300200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
46	chr7:25299400-25300400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr7:25299400-25300600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:25299400-25300600	Enhancers	Primary hematopoietic stem cells	blood
49	chr7:25299400-25300600	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr7:25299400-25300800	Enhancers	Fetal Stomach	stomach

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