Variant report

Variant	rs7954961
Chromosome Location	chr12:120286192-120286193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10744744	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10774517	0.95[CEU][hapmap];0.87[CHB][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10774518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10774519	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10849702	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849703	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11609520	0.95[JPT][hapmap]
rs203343	0.82[TSI][hapmap]
rs203352	0.82[JPT][hapmap]
rs2269938	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2269939	0.82[ASW][hapmap];0.81[GIH][hapmap]
rs3847958	0.82[ASW][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.83[YRI][hapmap]
rs6490271	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7309586	0.85[GIH][hapmap];0.83[YRI][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	nsv455727	chr12:120259679-120420670	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv560397	chr12:120259679-120420670	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv975612	chr12:120279837-120287876	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7954961	DIABLO	cis	cerebellum	SCAN
rs7954961	MLXIP	cis	cerebellum	SCAN
rs7954961	LRRC43	cis	parietal	SCAN
rs7954961	POP5	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120209400-120293600	Weak transcription	Primary T cells from cord blood	blood
2	chr12:120223000-120314400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:120242600-120293800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr12:120242600-120294400	Weak transcription	Fetal Kidney	kidney
5	chr12:120242800-120287800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:120243200-120288200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:120254800-120286400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr12:120254800-120314600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:120256600-120304000	Weak transcription	Fetal Heart	heart
10	chr12:120259200-120311800	Strong transcription	Dnd41	blood
11	chr12:120265200-120301800	Weak transcription	Osteobl	bone
12	chr12:120266400-120289200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:120270400-120314200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr12:120272000-120303600	Weak transcription	Fetal Lung	lung
15	chr12:120272200-120306800	Weak transcription	HSMM	muscle
16	chr12:120273200-120309000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:120274800-120306200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:120275600-120288800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:120275800-120288000	Weak transcription	HMEC	breast
20	chr12:120275800-120290400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:120276000-120307000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:120276200-120298600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr12:120276200-120300600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:120276400-120291600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:120276400-120292000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:120276600-120297400	Strong transcription	Thymus	Thymus
27	chr12:120277000-120288400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:120277000-120291200	Strong transcription	Fetal Thymus	thymus
29	chr12:120277000-120307200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:120277000-120314400	Weak transcription	Spleen	Spleen
31	chr12:120277200-120314600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr12:120277600-120303800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr12:120278400-120313800	Weak transcription	Brain Germinal Matrix	brain
34	chr12:120278600-120313800	Weak transcription	Fetal Brain Female	brain
35	chr12:120279400-120291000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:120279400-120301600	Weak transcription	Fetal Intestine Small	intestine
37	chr12:120279600-120303800	Weak transcription	Fetal Intestine Large	intestine
38	chr12:120279800-120314200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr12:120279800-120314400	Weak transcription	Primary B cells from cord blood	blood
40	chr12:120280200-120304400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:120280600-120286800	Strong transcription	A549	lung
42	chr12:120281200-120287800	Weak transcription	HepG2	liver
43	chr12:120281200-120290000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:120281200-120304400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:120281400-120288600	Weak transcription	NHDF-Ad	bronchial
46	chr12:120281400-120306400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:120281600-120286600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:120281600-120288600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:120282600-120288600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:120282800-120289800	Strong transcription	Fetal Stomach	stomach

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