Variant report

Variant	rs7968375
Chromosome Location	chr12:12502001-12502002
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12501597..12504303-chr12:12848029..12850251,2	K562	blood:
2	chr12:12501756..12503820-chr12:12509545..12511706,2	MCF-7	breast:
3	chr12:12501083..12504981-chr12:12508403..12511914,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205791	Chromatin interaction
ENSG00000183150	Chromatin interaction
ENSG00000165714	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11054833	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs11608549	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898807	chr12:12448948-12502001	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv898808	chr12:12463407-12549503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv898809	chr12:12488067-12509314	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7968375	ETV6	cis	cerebellum	SCAN
rs7968375	NACC2	trans	cerebellum	SCAN
rs7968375	LOH12CR1	cis	parietal	SCAN
rs7968375	LOH12CR1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12473800-12502400	Weak transcription	NHLF	lung
2	chr12:12480400-12502400	Weak transcription	Right Ventricle	heart
3	chr12:12481200-12502200	Weak transcription	Fetal Heart	heart
4	chr12:12481800-12502400	Weak transcription	Psoas Muscle	Psoas
5	chr12:12482400-12502200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:12483600-12502800	Weak transcription	Spleen	Spleen
7	chr12:12485400-12502400	Weak transcription	Esophagus	oesophagus
8	chr12:12485400-12502800	Weak transcription	Gastric	stomach
9	chr12:12485400-12502800	Weak transcription	Small Intestine	intestine
10	chr12:12487200-12502600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:12487400-12502200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:12487400-12502200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:12487600-12502200	Weak transcription	Colonic Mucosa	Colon
14	chr12:12489600-12502400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:12489600-12502600	Weak transcription	Placenta	Placenta
16	chr12:12489800-12502400	Weak transcription	Pancreas	Pancrea
17	chr12:12490800-12502400	Weak transcription	Brain Germinal Matrix	brain
18	chr12:12492000-12502400	Weak transcription	Aorta	Aorta
19	chr12:12492200-12502200	Weak transcription	Primary B cells from cord blood	blood
20	chr12:12492200-12502200	Weak transcription	Primary T cells from cord blood	blood
21	chr12:12492200-12502600	Weak transcription	Lung	lung
22	chr12:12492200-12502800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:12492400-12502600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr12:12494200-12502200	Weak transcription	Brain Substantia Nigra	brain
25	chr12:12494200-12502600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:12494400-12502800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr12:12495200-12502200	Weak transcription	Liver	Liver
28	chr12:12495200-12502200	Weak transcription	Fetal Brain Male	brain
29	chr12:12495200-12502600	Weak transcription	Left Ventricle	heart
30	chr12:12495400-12502600	Weak transcription	Ovary	ovary
31	chr12:12496200-12502800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:12496400-12502200	Weak transcription	Adipose Nuclei	Adipose
33	chr12:12498800-12502600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:12500400-12502800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:12501400-12502400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:12501400-12502400	Active TSS	Duodenum Mucosa	Duodenum
37	chr12:12501400-12503800	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr12:12501600-12502200	Active TSS	K562	blood
39	chr12:12501600-12502400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:12501600-12502800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:12501800-12502200	Enhancers	Brain Angular Gyrus	brain
42	chr12:12501800-12502200	Enhancers	Brain Cingulate Gyrus	brain
43	chr12:12501800-12502600	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr12:12501800-12504200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:12502000-12502200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
46	chr12:12502000-12502200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
47	chr12:12502000-12502200	Enhancers	Primary hematopoietic stem cells	blood
48	chr12:12502000-12502200	Enhancers	Brain Hippocampus Middle	brain
49	chr12:12502000-12502200	Enhancers	Colon Smooth Muscle	Colon
50	chr12:12502000-12502200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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