Variant report

Variant	rs10172624
Chromosome Location	chr2:9904037-9904038
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9695083..9696978-chr2:9901909..9904289,2	K562	blood:
2	chr2:9901768..9906137-chr2:9907161..9912624,7	K562	blood:
3	chr2:9902911..9905269-chr2:9908747..9910675,2	K562	blood:
4	chr2:9901947..9904351-chr2:9980319..9983166,2	K562	blood:
5	chr2:9897831..9899412-chr2:9902196..9904626,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243491	Chromatin interaction
ENSG00000151694	Chromatin interaction
ENSG00000271855	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1004488	1.00[AMR][1000 genomes]
rs10188428	1.00[AMR][1000 genomes]
rs10190680	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10200454	1.00[AMR][1000 genomes]
rs10208526	1.00[AMR][1000 genomes]
rs10469619	1.00[AMR][1000 genomes]
rs16867145	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4327210	1.00[AMR][1000 genomes]
rs6723929	1.00[AMR][1000 genomes]
rs6728922	1.00[AMR][1000 genomes]
rs73913171	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1014911	chr2:9863969-9905959	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv873618	chr2:9870631-9919759	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv873619	chr2:9870631-9956981	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv518227	chr2:9893454-9909114	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9898600-9904400	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:9898600-9905800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:9898600-9906000	Weak transcription	Lung	lung
4	chr2:9898600-9906200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:9898600-9906400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:9898600-9906400	Weak transcription	Placenta	Placenta
7	chr2:9898600-9906800	Enhancers	Fetal Muscle Leg	muscle
8	chr2:9899400-9909200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:9899600-9904800	Weak transcription	Esophagus	oesophagus
10	chr2:9899800-9905200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:9900400-9909400	Weak transcription	Brain Anterior Caudate	brain
12	chr2:9900800-9906200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:9901000-9906000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:9901000-9906000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:9901000-9906000	Weak transcription	HMEC	breast
16	chr2:9901200-9905800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:9901200-9905800	Weak transcription	NHEK	skin
18	chr2:9901200-9906800	Enhancers	Fetal Heart	heart
19	chr2:9901400-9904600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:9901400-9906200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:9901400-9909400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr2:9901400-9909400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:9901600-9906200	Weak transcription	Fetal Thymus	thymus
24	chr2:9901800-9910200	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:9902000-9906000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:9902200-9905800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:9902200-9906000	Weak transcription	Fetal Lung	lung
28	chr2:9902200-9906200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:9902400-9906000	Weak transcription	Fetal Brain Male	brain
30	chr2:9902600-9905200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:9903000-9904800	Enhancers	Pancreas	Pancrea
32	chr2:9903000-9911800	Enhancers	Fetal Intestine Small	intestine
33	chr2:9903200-9904200	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr2:9903200-9905000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:9903200-9906200	Enhancers	K562	blood
36	chr2:9903200-9912000	Enhancers	Fetal Intestine Large	intestine
37	chr2:9903400-9904600	Bivalent Enhancer	HepG2	liver
38	chr2:9903600-9904200	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr2:9903600-9904400	Enhancers	Osteobl	bone
40	chr2:9903600-9906200	Weak transcription	Right Atrium	heart
41	chr2:9903600-9906400	Weak transcription	Right Ventricle	heart
42	chr2:9903600-9906800	Enhancers	A549	lung
43	chr2:9903600-9910400	Weak transcription	Psoas Muscle	Psoas
44	chr2:9903600-9910800	Weak transcription	Left Ventricle	heart
45	chr2:9903800-9904200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:9903800-9904600	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr2:9903800-9904600	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr2:9903800-9904800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:9903800-9905600	Enhancers	GM12878-XiMat	blood
50	chr2:9903800-9905800	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links