Variant report

Variant	rs7957338
Chromosome Location	chr12:11921305-11921306
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:11801832..11803757-chr12:11920063..11922984,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139083	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10491990	0.81[CHD][hapmap];0.80[JPT][hapmap]
rs10772506	0.87[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs11054456	0.80[JPT][hapmap]
rs1986946	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3782139	0.86[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.96[ASN][1000 genomes]
rs4763725	0.87[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs4763726	0.84[JPT][hapmap]
rs60587284	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7311993	0.87[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs7973524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
2	nsv1053609	chr12:11898099-11933906	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv469113	chr12:11913360-11931259	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv557574	chr12:11913360-11931259	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv469114	chr12:11916908-11929481	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv557575	chr12:11916908-11929481	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7957338	ARHGDIB	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11908600-11931800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:11909600-11932400	Genic enhancers	Fetal Thymus	thymus
3	chr12:11914400-11921600	Enhancers	Primary B cells from peripheral blood	blood
4	chr12:11914400-11925400	Genic enhancers	Dnd41	blood
5	chr12:11914400-11925800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:11914800-11923600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr12:11915400-11938000	Weak transcription	NHEK	skin
8	chr12:11915600-11921800	Enhancers	Fetal Muscle Leg	muscle
9	chr12:11915600-11938000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:11916600-11922000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr12:11916800-11921400	Enhancers	Thymus	Thymus
12	chr12:11916800-11921600	Enhancers	Brain Hippocampus Middle	brain
13	chr12:11917400-11922000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:11918000-11923600	Enhancers	Adipose Nuclei	Adipose
15	chr12:11918000-11923800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:11918000-11936000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:11918400-11921600	Enhancers	Fetal Intestine Large	intestine
18	chr12:11918800-11922000	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr12:11919000-11921600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr12:11919000-11921600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:11919000-11921800	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr12:11919000-11923200	Weak transcription	Right Ventricle	heart
23	chr12:11919000-11923400	Enhancers	Duodenum Mucosa	Duodenum
24	chr12:11919400-11921600	Enhancers	HUVEC	blood vessel
25	chr12:11919400-11923800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:11919400-11926800	Enhancers	Primary hematopoietic stem cells	blood
27	chr12:11919400-11935000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:11919600-11921400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:11919600-11921400	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr12:11919600-11921600	Enhancers	Primary T cells from cord blood	blood
31	chr12:11919600-11922000	Enhancers	Fetal Intestine Small	intestine
32	chr12:11919600-11922600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:11919600-11922800	Weak transcription	Esophagus	oesophagus
34	chr12:11919600-11924000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:11919600-11926800	Weak transcription	Psoas Muscle	Psoas
36	chr12:11919600-11927600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:11919600-11932000	Weak transcription	HSMM	muscle
38	chr12:11919600-11936200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr12:11919600-11936800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:11919800-11921400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:11919800-11921400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:11919800-11921400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:11919800-11921400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:11919800-11921400	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr12:11919800-11921400	Enhancers	Stomach Smooth Muscle	stomach
46	chr12:11919800-11921600	Enhancers	Colon Smooth Muscle	Colon
47	chr12:11919800-11921800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:11919800-11921800	Enhancers	Fetal Kidney	kidney
49	chr12:11919800-11922600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:11919800-11922600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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