Variant report

Variant	rs7137734
Chromosome Location	chr12:25350122-25350123
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	chr12:25347604-25351824	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:25350000-25350376	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:25349919..25351633-chr12:25538226..25540199,2	K562	blood:
2	chr12:25347765..25350303-chr12:25380801..25383112,2	K562	blood:
3	chr12:25349644..25351670-chr12:25539311..25540957,2	MCF-7	breast:

Variant related genes	Relation type
CASC1	TF binding region
ENSG00000268076	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11047903	0.87[AFR][1000 genomes]
rs12814233	0.82[JPT][hapmap]
rs7960917	1.00[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7973450	0.84[MKK][hapmap]

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	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7137734	SSPN	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25348600-25360000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:25348600-25402200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:25348600-25403200	Weak transcription	Spleen	Spleen
4	chr12:25348800-25355400	Weak transcription	Small Intestine	intestine
5	chr12:25348800-25359400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:25348800-25360200	Weak transcription	Esophagus	oesophagus
7	chr12:25349000-25353400	Weak transcription	HSMMtube	muscle
8	chr12:25349000-25353800	Weak transcription	Pancreas	Pancrea
9	chr12:25349000-25355200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr12:25349000-25356000	Weak transcription	Placenta	Placenta
11	chr12:25349000-25357600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:25349000-25360000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:25349000-25360000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:25349000-25360400	Weak transcription	Psoas Muscle	Psoas
15	chr12:25349000-25369200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:25349000-25372800	Weak transcription	Aorta	Aorta
17	chr12:25349000-25374200	Weak transcription	Lung	lung
18	chr12:25349000-25386000	Weak transcription	Left Ventricle	heart
19	chr12:25349000-25402400	Weak transcription	Right Ventricle	heart
20	chr12:25349200-25350200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr12:25349200-25352400	Weak transcription	Fetal Thymus	thymus
22	chr12:25349200-25353600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:25349200-25353600	Weak transcription	HMEC	breast
24	chr12:25349200-25353600	Weak transcription	NHDF-Ad	bronchial
25	chr12:25349200-25353800	Weak transcription	HSMM	muscle
26	chr12:25349200-25355400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:25349200-25356000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:25349200-25356200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr12:25349200-25359000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr12:25349200-25359400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:25349200-25360800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr12:25349200-25362400	Weak transcription	Colonic Mucosa	Colon
33	chr12:25349200-25363200	Weak transcription	Brain Substantia Nigra	brain
34	chr12:25349200-25363400	Weak transcription	Stomach Mucosa	stomach
35	chr12:25349400-25350400	Weak transcription	Primary B cells from cord blood	blood
36	chr12:25349400-25353400	Weak transcription	Osteobl	bone
37	chr12:25349400-25353600	Weak transcription	HUVEC	blood vessel
38	chr12:25349400-25353600	Weak transcription	NHEK	skin
39	chr12:25349400-25353800	Weak transcription	Primary T cells from cord blood	blood
40	chr12:25349400-25353800	Weak transcription	Right Atrium	heart
41	chr12:25349400-25355400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr12:25349400-25356000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr12:25349400-25356200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:25349400-25356200	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:25349400-25356400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:25349400-25357200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:25349400-25357600	Weak transcription	Adipose Nuclei	Adipose
48	chr12:25349400-25359800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:25349400-25367400	Weak transcription	Fetal Stomach	stomach
50	chr12:25349400-25388200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links