Variant report

Variant	rs10497475
Chromosome Location	chr2:179002948-179002949
allele	C/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	POLR2A	chr2:179001004-179003397	K562	blood:	n/a	n/a
2	POLR2A	chr2:179001969-179003414	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:179001333..179003104-chr2:179278827..179280728,2	MCF-7	breast:
2	chr2:178998158..179000091-chr2:179001062..179003808,2	K562	blood:
3	chr2:178993079..178995697-chr2:179002423..179004658,2	K562	blood:

Variant related genes	Relation type
RNU5E-9P	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10174910	1.00[JPT][hapmap]
rs10205083	1.00[JPT][hapmap]
rs11894754	1.00[JPT][hapmap]
rs12994312	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12996084	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12997449	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13022619	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs13030533	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs168009	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16866058	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16866088	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16866108	1.00[ASN][1000 genomes]
rs16866151	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16866156	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16866169	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17695382	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs17695415	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1898012	1.00[MKK][hapmap]
rs334053	0.82[ASN][1000 genomes]
rs34402025	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35211706	0.80[AMR][1000 genomes]
rs35994691	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs66558684	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726222	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs67941002	1.00[AFR][1000 genomes]
rs71423556	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178978000-179003200	Weak transcription	Spleen	Spleen
2	chr2:178978000-179003800	Weak transcription	Aorta	Aorta
3	chr2:178978000-179016400	Weak transcription	Gastric	stomach
4	chr2:178978600-179003000	Weak transcription	Right Ventricle	heart
5	chr2:178978600-179003600	Weak transcription	Fetal Heart	heart
6	chr2:178978800-179004000	Weak transcription	Brain Germinal Matrix	brain
7	chr2:178979000-179005400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:178987200-179005800	Weak transcription	Psoas Muscle	Psoas
9	chr2:178987800-179017000	Weak transcription	Fetal Lung	lung
10	chr2:178990200-179007000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:178990400-179003000	Weak transcription	HMEC	breast
12	chr2:178990800-179003800	Weak transcription	GM12878-XiMat	blood
13	chr2:178991000-179009600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:178991200-179007400	Weak transcription	Osteobl	bone
15	chr2:178991800-179003600	Weak transcription	Left Ventricle	heart
16	chr2:178992200-179003000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:178992400-179003200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:178992400-179007800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:178993200-179016800	Weak transcription	Fetal Intestine Small	intestine
20	chr2:178994400-179003000	Weak transcription	Fetal Intestine Large	intestine
21	chr2:178994400-179003600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:178994400-179007200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:178994400-179007200	Weak transcription	HSMMtube	muscle
24	chr2:178994600-179004000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:178994600-179004200	Weak transcription	Brain Anterior Caudate	brain
26	chr2:178994600-179005800	Weak transcription	Liver	Liver
27	chr2:178994600-179007000	Weak transcription	Fetal Kidney	kidney
28	chr2:178995400-179003400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr2:178995800-179003600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:178997800-179006800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:178997800-179008200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:178999600-179004200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:178999800-179003400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:179000200-179003800	Weak transcription	Dnd41	blood
35	chr2:179000200-179006000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:179000200-179007200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:179000400-179003600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:179000400-179004000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:179000400-179005600	Weak transcription	A549	lung
40	chr2:179000400-179007200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:179000600-179004800	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:179001400-179003400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:179001400-179003600	Weak transcription	Fetal Thymus	thymus
44	chr2:179001400-179005000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:179001600-179003200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:179001600-179003600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:179001600-179003800	Weak transcription	Fetal Muscle Leg	muscle
48	chr2:179001600-179003800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr2:179001600-179004000	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr2:179001600-179007200	Weak transcription	HSMM	muscle

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