Variant report

Variant	rs7029812
Chromosome Location	chr9:79307280-79307281
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	USF1	chr9:79306869-79307383	SK-N-SH_RA	brain:	n/a	n/a
2	POLR2A	chr9:79306867-79307294	SK-N-SH	brain:	n/a	n/a
3	YY1	chr9:79306884-79307282	SK-N-SH_RA	brain:	n/a	chr9:79307092-79307104
4	USF1	chr9:79306831-79307382	SK-N-SH	brain:	n/a	n/a
5	USF1	chr9:79306903-79307337	HCT-116	colon:	n/a	n/a
6	REST	chr9:79306570-79307336	H1-neurons	neurons:	n/a	chr9:79306753-79306766
7	YY1	chr9:79306800-79307297	SK-N-SH_RA	brain:	n/a	chr9:79307092-79307104 chr9:79306837-79306848
8	USF1	chr9:79306812-79307407	H1-hESC	embryonic stem cell:	n/a	n/a
9	ZNF263	chr9:79306837-79307571	HEK293-T-REx	kidney:	n/a	n/a
10	USF2	chr9:79306854-79307317	H1-hESC	embryonic stem cell:	n/a	n/a
11	USF1	chr9:79306859-79307347	H1-hESC	embryonic stem cell:	n/a	n/a
12	TAF1	chr9:79306813-79307297	H1-neurons	neurons:	n/a	n/a
13	USF1	chr9:79306757-79307376	HCT-116	colon:	n/a	n/a
14	POLR2A	chr9:79306671-79307283	H1-neurons	neurons:	n/a	n/a
15	USF1	chr9:79306731-79307447	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79307128..79309630-chr9:79312231..79313981,2	MCF-7	breast:

Variant related genes	Relation type
PRUNE2	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10512060	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11145015	1.00[MEX][hapmap]
rs12339310	1.00[CHB][hapmap]
rs12346312	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17180718	1.00[CHB][hapmap]
rs17180920	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs17180962	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs17786994	1.00[CHB][hapmap]
rs56919429	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893481	chr9:79304043-79348193	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79300400-79332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:79304200-79307800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:79305000-79307600	Weak transcription	Aorta	Aorta
4	chr9:79305200-79307600	Enhancers	Stomach Mucosa	stomach
5	chr9:79306000-79307600	Active TSS	Fetal Brain Female	brain
6	chr9:79306000-79307800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:79306000-79307800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr9:79306000-79307800	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr9:79306400-79307400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr9:79306400-79307400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr9:79306400-79307400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr9:79306400-79307400	Active TSS	Fetal Brain Male	brain
13	chr9:79306400-79307400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr9:79306600-79307400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr9:79306600-79307400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr9:79306600-79307400	Active TSS	Primary T cells from cord blood	blood
17	chr9:79306600-79307400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr9:79306600-79307400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:79306600-79307400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr9:79306600-79307400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr9:79306600-79307400	Flanking Active TSS	HUVEC	blood vessel
22	chr9:79306600-79307600	Flanking Active TSS	Osteobl	bone
23	chr9:79306600-79307800	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr9:79306600-79307800	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr9:79306600-79307800	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr9:79306600-79308000	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr9:79306600-79308000	Enhancers	Gastric	stomach
28	chr9:79306800-79307400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:79306800-79307400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr9:79306800-79307400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
31	chr9:79306800-79307400	Flanking Active TSS	Fetal Intestine Small	intestine
32	chr9:79306800-79307400	Flanking Active TSS	Fetal Muscle Leg	muscle
33	chr9:79306800-79307400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
34	chr9:79306800-79307600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:79306800-79307600	Active TSS	Brain Germinal Matrix	brain
36	chr9:79306800-79307600	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr9:79306800-79307800	Enhancers	Pancreas	Pancrea
38	chr9:79306800-79308000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr9:79307000-79307400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
40	chr9:79307000-79307400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:79307000-79307400	Flanking Active TSS	Fetal Thymus	thymus
42	chr9:79307000-79307400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
43	chr9:79307000-79307400	Flanking Active TSS	NHDF-Ad	bronchial
44	chr9:79307000-79307800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr9:79307000-79307800	Enhancers	Primary hematopoietic stem cells	blood
46	chr9:79307200-79307400	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr9:79307200-79307400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:79307200-79307400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:79307200-79307400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr9:79307200-79307400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell

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