Variant report

Variant	rs17021360
Chromosome Location	chr3:28360679-28360680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:28354861..28358601-chr3:28360600..28365308,4	K562	blood:
2	chr3:28360111..28361698-chr3:28390791..28393091,2	K562	blood:
3	chr3:28338220..28341133-chr3:28359102..28361875,2	K562	blood:
4	chr3:28359320..28360886-chr3:28367383..28369282,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CMC1-3	chr3:28357824-28361253	NONHSAT088780

Variant related genes	Relation type
ENSG00000187118	Chromatin interaction
ENSG00000163512	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs17021351	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17021353	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17021368	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17021371	1.00[ASW][hapmap];0.89[MKK][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17021372	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17021374	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17029779	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6800120	1.00[MEX][hapmap]
rs7639746	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7643610	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7651491	1.00[AMR][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	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28314400-28365400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:28315000-28363000	Weak transcription	A549	lung
3	chr3:28317600-28380000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:28317600-28389400	Weak transcription	Esophagus	oesophagus
5	chr3:28326400-28365400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:28332800-28362400	Weak transcription	Primary B cells from cord blood	blood
7	chr3:28332800-28365200	Weak transcription	HSMMtube	muscle
8	chr3:28332800-28365400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:28337200-28365200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:28337400-28361000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:28337400-28363000	Weak transcription	GM12878-XiMat	blood
12	chr3:28337600-28361000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:28338200-28364000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:28343800-28383800	Weak transcription	Aorta	Aorta
15	chr3:28348600-28365200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:28349000-28365400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:28349400-28364200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:28349400-28365600	Weak transcription	Psoas Muscle	Psoas
19	chr3:28349600-28365400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:28349800-28389400	Weak transcription	Gastric	stomach
21	chr3:28350000-28363800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:28350000-28376800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:28350200-28361600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:28350400-28365400	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:28351200-28366600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:28351400-28365600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:28351400-28366800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr3:28354200-28364600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:28354800-28363000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:28354800-28365600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:28356000-28361400	Weak transcription	NHDF-Ad	bronchial
32	chr3:28356000-28364000	Weak transcription	Brain Substantia Nigra	brain
33	chr3:28356800-28376800	Weak transcription	Ovary	ovary
34	chr3:28357200-28365600	Weak transcription	Colonic Mucosa	Colon
35	chr3:28357400-28366200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:28357400-28366600	Weak transcription	Fetal Brain Male	brain
37	chr3:28357600-28361600	Weak transcription	HepG2	liver
38	chr3:28357600-28365600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:28357600-28370400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr3:28357800-28362400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr3:28357800-28362800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:28357800-28365600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:28358400-28366600	Weak transcription	Fetal Heart	heart
44	chr3:28358600-28365000	Weak transcription	Hela-S3	cervix
45	chr3:28358600-28365400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr3:28358600-28365600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr3:28358600-28367000	Weak transcription	HMEC	breast
48	chr3:28358600-28386400	Weak transcription	Thymus	Thymus
49	chr3:28358800-28361000	Weak transcription	Fetal Thymus	thymus
50	chr3:28358800-28361600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links