Variant report

Variant	rs2970477
Chromosome Location	chr7:101586766-101586767
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:101584833..101587634-chr7:101667426..101668972,2	MCF-7	breast:
2	chr7:101524980..101528234-chr7:101584443..101587218,5	MCF-7	breast:
3	chr7:101498814..101500323-chr7:101586535..101589205,2	K562	blood:
4	chr7:101586542..101589464-chr7:101627667..101631970,4	MCF-7	breast:
5	chr7:101574113..101579725-chr7:101580632..101589310,14	MCF-7	breast:
6	chr7:101455300..101463809-chr7:101582792..101593292,40	MCF-7	breast:
7	chr7:101524538..101530208-chr7:101583819..101590225,13	MCF-7	breast:
8	chr7:101584102..101588182-chr7:101600791..101605094,5	MCF-7	breast:
9	chr7:101586382..101587949-chr7:101645381..101648210,2	MCF-7	breast:
10	chr7:101584411..101586887-chr7:101593987..101597254,4	MCF-7	breast:
11	chr7:101574246..101577081-chr7:101585264..101587735,2	MCF-7	breast:
12	chr7:101585552..101588102-chr7:101621880..101624253,3	MCF-7	breast:
13	chr7:101582848..101590446-chr7:101646237..101653992,20	MCF-7	breast:
14	chr7:101574397..101581279-chr7:101584061..101589887,8	K562	blood:
15	chr7:101585477..101587144-chr7:101767345..101769939,2	MCF-7	breast:
16	chr7:101586695..101588512-chr7:101590160..101592352,2	K562	blood:
17	chr7:101582741..101590045-chr7:101612112..101621417,29	MCF-7	breast:
18	chr7:101511680..101514939-chr7:101582566..101587455,5	MCF-7	breast:
19	chr7:101457338..101463673-chr7:101582596..101588609,15	MCF-7	breast:
20	chr7:101585316..101588407-chr7:101614430..101618418,4	MCF-7	breast:
21	chr7:101583996..101590317-chr7:101598825..101610404,14	MCF-7	breast:
22	chr7:101583393..101585802-chr7:101586668..101590490,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction
ENSG00000272219	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs2906649	0.80[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2906653	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2970478	0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2970493	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2970494	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs385854	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404284	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs414438	0.88[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap]
rs425964	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs427039	0.94[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs433736	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs434564	0.87[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs439124	0.81[JPT][hapmap]
rs440923	0.85[ASN][1000 genomes]
rs441601	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs441780	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4729764	0.91[ASN][1000 genomes]
rs727544	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs740302	0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs876826	0.82[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]

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	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv482846	chr7:101539981-101707666	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv888827	chr7:101562674-101650302	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101567000-101596000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr7:101570200-101597000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:101571600-101587400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr7:101575800-101587400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr7:101577600-101595600	Weak transcription	Primary T cells from cord blood	blood
6	chr7:101578200-101612000	Weak transcription	HepG2	liver
7	chr7:101578200-101671200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:101580400-101587600	Weak transcription	Spleen	Spleen
9	chr7:101580600-101590600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr7:101580600-101590800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr7:101580600-101591200	Weak transcription	Brain Substantia Nigra	brain
12	chr7:101583400-101587600	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr7:101583400-101587800	Enhancers	Fetal Thymus	thymus
14	chr7:101583400-101608000	Weak transcription	Primary B cells from cord blood	blood
15	chr7:101583600-101587400	Enhancers	Fetal Stomach	stomach
16	chr7:101583600-101587800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:101583600-101589400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr7:101583600-101589600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr7:101583600-101591000	Enhancers	Fetal Heart	heart
20	chr7:101584000-101587000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:101584000-101587000	Genic enhancers	Fetal Intestine Small	intestine
22	chr7:101584000-101587800	Enhancers	Right Atrium	heart
23	chr7:101584000-101589400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr7:101584400-101590600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:101584400-101596200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr7:101584600-101587400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:101584600-101588800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr7:101584800-101590800	Weak transcription	Fetal Brain Female	brain
29	chr7:101585000-101587600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr7:101585000-101590000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr7:101585200-101587400	Weak transcription	Brain Germinal Matrix	brain
32	chr7:101585200-101588000	Enhancers	Colon Smooth Muscle	Colon
33	chr7:101585200-101590800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr7:101585400-101589400	Enhancers	Rectal Smooth Muscle	rectum
35	chr7:101585400-101590800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr7:101585600-101586800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr7:101585600-101587000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:101585600-101588000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr7:101585600-101588000	Weak transcription	Dnd41	blood
40	chr7:101585600-101588800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr7:101585600-101589200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr7:101585600-101590000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr7:101585600-101590600	Weak transcription	Fetal Lung	lung
44	chr7:101585600-101591000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr7:101585600-101591000	Weak transcription	Brain Anterior Caudate	brain
46	chr7:101585600-101594400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr7:101585800-101587400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr7:101585800-101587400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:101585800-101587800	Enhancers	Lung	lung
50	chr7:101585800-101590800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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