Variant report

Variant	rs2623099
Chromosome Location	chr3:136265134-136265135
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136263152..136267364-chr3:136469698..136472182,6	MCF-7	breast:
2	chr3:136264178..136265425-chr3:136470257..136471763,14	MCF-7	breast:
3	chr3:136264021..136266298-chr3:136470657..136471752,36	MCF-7	breast:
4	chr3:136262930..136265454-chr3:136470250..136473086,3	K562	blood:
5	chr3:136257749..136260401-chr3:136264258..136266069,2	MCF-7	breast:
6	chr3:136263091..136265454-chr3:136470690..136473476,4	K562	blood:
7	chr3:136262189..136267900-chr3:136469121..136472269,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11707691	1.00[LWK][hapmap]
rs13067764	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2655009	1.00[LWK][hapmap]
rs2880501	1.00[MKK][hapmap]
rs8179993	1.00[LWK][hapmap]
rs9826828	1.00[CHB][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv877528	chr3:136209550-136295283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv591850	chr3:136209550-136300732	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136176800-136266200	Weak transcription	Hela-S3	cervix
3	chr3:136191400-136268000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:136195400-136278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:136220600-136266200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:136222400-136266200	Weak transcription	HSMM	muscle
9	chr3:136246600-136286200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:136247200-136319800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:136247200-136334800	Weak transcription	Aorta	Aorta
12	chr3:136247400-136270600	Weak transcription	Fetal Thymus	thymus
13	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:136251400-136319000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr3:136251600-136266000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:136251600-136270400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:136251600-136284400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:136251600-136284400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:136251600-136289400	Weak transcription	Adipose Nuclei	Adipose
20	chr3:136251600-136322400	Weak transcription	Liver	Liver
21	chr3:136251800-136266400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:136251800-136284800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:136252000-136270000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:136252600-136266200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:136252600-136284800	Weak transcription	Left Ventricle	heart
26	chr3:136252600-136320400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:136252800-136266000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:136252800-136305600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:136252800-136314800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:136255200-136294000	Weak transcription	Primary T cells from cord blood	blood
31	chr3:136255800-136291600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:136256800-136266200	Weak transcription	NHDF-Ad	bronchial
33	chr3:136257600-136267800	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:136257600-136270000	Weak transcription	Fetal Stomach	stomach
35	chr3:136257600-136282800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:136258000-136269800	Weak transcription	Fetal Intestine Small	intestine
37	chr3:136258200-136275400	Weak transcription	Fetal Intestine Large	intestine
38	chr3:136259000-136269800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:136261000-136269600	Weak transcription	Dnd41	blood
40	chr3:136262600-136266000	Weak transcription	Primary B cells from cord blood	blood
41	chr3:136262800-136266200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:136263000-136327200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:136263200-136266000	Weak transcription	HUVEC	blood vessel
44	chr3:136263200-136272000	Weak transcription	Stomach Mucosa	stomach
45	chr3:136263400-136266200	Weak transcription	NHLF	lung
46	chr3:136263600-136265400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:136263800-136266200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:136263800-136266200	Weak transcription	NH-A	brain
49	chr3:136263800-136277600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:136264000-136266000	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links