Variant report

Variant	rs2605379
Chromosome Location	chr12:74936668-74936669
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:74931110-74940575	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:74936287-74937111	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:74934898-74938452	K562	blood:	n/a	n/a
4	POLR2A	chr12:74932912-74937655	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr12:74934609-74937472	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:74931035-74936789	IMR90	lung:	n/a	n/a
7	POLR2A	chr12:74931091-74937173	GM12891	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:74934644..74937630-chr12:74950063..74952451,3	MCF-7	breast:
2	chr12:74819585..74822514-chr12:74935420..74937697,2	K562	blood:
3	chr12:74933499..74938752-chr12:74938991..74943644,10	K562	blood:
4	chr12:74934893..74937822-chr12:74975475..74977928,2	MCF-7	breast:
5	chr12:74920482..74922543-chr12:74935619..74938584,2	MCF-7	breast:
6	chr12:74929601..74933992-chr12:74933997..74938801,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000257386	TF binding region
ENSG00000253719	Chromatin interaction
ENSG00000257386	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1037887	1.00[AFR][1000 genomes]
rs1389486	0.83[AFR][1000 genomes]
rs1389487	0.83[AFR][1000 genomes]
rs1389489	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1389490	1.00[AFR][1000 genomes]
rs1389491	1.00[AFR][1000 genomes]
rs1493798	1.00[AFR][1000 genomes]
rs1493804	1.00[AFR][1000 genomes]
rs1493807	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1563930	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1870699	1.00[AFR][1000 genomes]
rs1873987	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs1873988	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2007674	1.00[AFR][1000 genomes]
rs2029717	1.00[AFR][1000 genomes]
rs2219608	1.00[AFR][1000 genomes]
rs2249335	0.83[AFR][1000 genomes]
rs2252250	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2605360	1.00[AFR][1000 genomes]
rs2605380	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2613880	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2613892	1.00[AFR][1000 genomes]
rs2613896	1.00[AFR][1000 genomes]
rs2613899	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2641465	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2925223	1.00[AFR][1000 genomes]
rs2925224	1.00[AFR][1000 genomes]
rs2926807	1.00[AFR][1000 genomes]
rs588875	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs590166	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs596999	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs625531	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs663854	1.00[AFR][1000 genomes]
rs694314	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs822806	1.00[YRI][hapmap]
rs822809	1.00[YRI][hapmap]
rs922222	0.83[AFR][1000 genomes]
rs970236	1.00[AFR][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	nsv1039468	chr12:74080586-75000246	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv899293	chr12:74835107-74995760	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv899295	chr12:74854750-74984992	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv470303	chr12:74880668-74945356	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	n/a
5	nsv899296	chr12:74880668-74974630	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:74933800-74937000	Weak transcription	Esophagus	oesophagus
2	chr12:74933800-74942800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:74934200-74942000	Weak transcription	Ovary	ovary
4	chr12:74934400-74938400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:74934600-74937600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:74934600-74937600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:74934600-74940800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:74934800-74936800	Genic enhancers	Primary B cells from cord blood	blood
9	chr12:74935000-74937000	Weak transcription	Brain Angular Gyrus	brain
10	chr12:74935200-74936800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:74935200-74936800	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:74935200-74936800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:74935200-74937600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:74935200-74938200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:74935200-74940800	Weak transcription	Pancreas	Pancrea
16	chr12:74935200-74941000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:74935200-74941800	Weak transcription	Thymus	Thymus
18	chr12:74935200-74942200	Weak transcription	Psoas Muscle	Psoas
19	chr12:74935200-74942600	Weak transcription	Small Intestine	intestine
20	chr12:74935200-74943600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:74935200-74945000	Weak transcription	Left Ventricle	heart
22	chr12:74935400-74937000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:74935400-74937000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
24	chr12:74935400-74942600	Weak transcription	Fetal Intestine Small	intestine
25	chr12:74935600-74936800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr12:74935600-74936800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:74935600-74937200	Strong transcription	HMEC	breast
28	chr12:74935600-74937400	Weak transcription	K562	blood
29	chr12:74935600-74937600	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr12:74935600-74937600	Weak transcription	HUVEC	blood vessel
31	chr12:74935600-74937800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr12:74935600-74938000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr12:74935600-74939000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:74935600-74941000	Weak transcription	Fetal Stomach	stomach
35	chr12:74935600-74941400	Weak transcription	Adipose Nuclei	Adipose
36	chr12:74935600-74942000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:74935600-74942400	Weak transcription	NHDF-Ad	bronchial
38	chr12:74935600-74943200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:74935800-74936800	Weak transcription	NH-A	brain
40	chr12:74935800-74936800	Weak transcription	Osteobl	bone
41	chr12:74935800-74937000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr12:74935800-74939400	Weak transcription	A549	lung
43	chr12:74935800-74940400	Weak transcription	Hela-S3	cervix
44	chr12:74935800-74941000	Weak transcription	Fetal Muscle Leg	muscle
45	chr12:74935800-74942800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:74936000-74936800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:74936000-74936800	Strong transcription	Primary B cells from peripheral blood	blood
48	chr12:74936000-74937000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr12:74936000-74937600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:74936000-74937600	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links