Variant report

Variant	rs7298031
Chromosome Location	chr12:29470266-29470267
allele	G/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	GATA3	chr12:29469398-29470286	SK-N-SH	brain:	n/a	chr12:29469600-29469609
2	GATA3	chr12:29469502-29470282	SK-N-SH	brain:	n/a	chr12:29469600-29469609
3	EP300	chr12:29469470-29470274	SK-N-SH	brain:	n/a	n/a
4	MEF2A	chr12:29469518-29470267	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr12:29469567-29470294	SK-N-SH	brain:	n/a	n/a
6	TEAD4	chr12:29469665-29470272	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
FAR2	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1006410	0.82[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1072724	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10743652	0.87[YRI][hapmap]
rs10743656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771517	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843376	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10843385	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11050168	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs12301475	0.82[AFR][1000 genomes]
rs12578931	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs12581107	0.83[AMR][1000 genomes]
rs17715086	0.82[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2016832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288128	0.82[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2288129	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2350315	0.80[EUR][1000 genomes]
rs3782505	0.82[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3782510	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4277150	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6487807	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299283	0.81[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7308534	0.92[YRI][hapmap]
rs7313552	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7315346	0.92[AFR][1000 genomes]
rs7358667	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7953619	1.00[YRI][hapmap]
rs7956305	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7961943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964831	0.82[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7980218	0.96[CEU][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986072	0.85[AMR][1000 genomes];0.85[EUR][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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv1795347	chr12:29458556-29471835	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7298031	RP11-996F15.2	cis	lung	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29426800-29472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
3	chr12:29449600-29470800	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:29452800-29494200	Weak transcription	Lung	lung
5	chr12:29453000-29472800	Weak transcription	Fetal Intestine Large	intestine
6	chr12:29453800-29480000	Weak transcription	Gastric	stomach
7	chr12:29454600-29475800	Weak transcription	Spleen	Spleen
8	chr12:29455200-29489400	Weak transcription	Primary B cells from cord blood	blood
9	chr12:29456600-29471000	Weak transcription	Fetal Intestine Small	intestine
10	chr12:29457600-29470600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:29459400-29471400	Weak transcription	Liver	Liver
12	chr12:29459400-29493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:29459600-29472800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:29459600-29476000	Weak transcription	Fetal Thymus	thymus
15	chr12:29460200-29476000	Weak transcription	Fetal Stomach	stomach
16	chr12:29461200-29486200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
18	chr12:29463600-29474600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:29463800-29475400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr12:29464000-29476000	Weak transcription	Fetal Kidney	kidney
21	chr12:29464600-29474800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:29465000-29494200	Weak transcription	Colonic Mucosa	Colon
23	chr12:29465600-29471000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:29465800-29472800	Weak transcription	NHDF-Ad	bronchial
25	chr12:29466000-29470400	Weak transcription	Dnd41	blood
26	chr12:29466000-29474400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:29466000-29474600	Weak transcription	Placenta	Placenta
28	chr12:29466200-29470600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:29466200-29470600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr12:29466200-29472600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr12:29466200-29488800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:29467200-29470800	Active TSS	Right Ventricle	heart
33	chr12:29467200-29472800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr12:29467200-29473400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr12:29467200-29475800	Weak transcription	Pancreas	Pancrea
36	chr12:29467400-29470800	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr12:29467600-29470600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr12:29467800-29470800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:29467800-29474600	Weak transcription	Adipose Nuclei	Adipose
40	chr12:29468200-29470600	Enhancers	Fetal Heart	heart
41	chr12:29468600-29470600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr12:29468600-29471800	Weak transcription	Left Ventricle	heart
43	chr12:29468600-29491000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:29468800-29470600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:29469000-29470800	Enhancers	Osteobl	bone
46	chr12:29469200-29471400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:29469400-29470600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:29469400-29470800	Active TSS	Right Atrium	heart
49	chr12:29469400-29470800	Enhancers	NH-A	brain
50	chr12:29469400-29471000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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