Variant report

Variant	rs35801460
Chromosome Location	chr12:49180828-49180829
allele	A/G
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	chr12:49180645-49180885	SH-SY5Y	brain:	n/a	n/a
2	NR2F2	chr12:49180403-49180884	MCF-7	breast:	n/a	chr12:49180526-49180541
3	POLR2A	chr12:49180812-49180902	HepG2	liver:	n/a	n/a
4	CEBPB	chr12:49180733-49180885	K562	blood:	n/a	n/a
5	GATA2	chr12:49180805-49181169	SH-SY5Y	brain:	n/a	chr12:49181013-49181023 chr12:49181016-49181025 chr12:49181015-49181025 chr12:49181016-49181023 chr12:49181016-49181023 chr12:49181009-49181030 chr12:49181016-49181023 chr12:49181017-49181034
6	CEBPB	chr12:49180685-49180953	IMR90	lung:	n/a	n/a
7	MXI1	chr12:49180368-49183259	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49179602..49181773-chr12:49197914..49199450,2	K562	blood:
2	chr12:49074389..49076545-chr12:49180456..49183753,3	MCF-7	breast:
3	chr12:49074245..49078609-chr12:49180778..49182867,4	MCF-7	breast:
4	chr12:49180246..49182305-chr12:49186657..49190531,5	MCF-7	breast:
5	chr12:49175402..49178124-chr12:49180679..49183666,2	K562	blood:
6	chr12:49178102..49185044-chr12:49204782..49211867,14	MCF-7	breast:
7	chr12:49180478..49186692-chr12:49206898..49214052,14	MCF-7	breast:
8	chr12:49160841..49162680-chr12:49178634..49181167,2	MCF-7	breast:
9	chr12:49165064..49172292-chr12:49177951..49185171,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257660	TF binding region
ADCY6	TF binding region
ENSG00000167535	Chromatin interaction
ENSG00000264201	Chromatin interaction
ENSG00000174233	Chromatin interaction
ENSG00000139620	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10875874	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875875	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168734	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168736	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168737	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168738	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168739	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168740	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168742	0.86[ASN][1000 genomes]
rs12306165	0.86[ASN][1000 genomes]
rs12314663	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12319012	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35468640	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3730069	1.00[ASN][1000 genomes]
rs3730070	1.00[ASN][1000 genomes]
rs3730072	1.00[ASN][1000 genomes]
rs3730074	1.00[ASN][1000 genomes]
rs68003719	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307701	0.86[ASN][1000 genomes]
rs9668292	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv826363	chr12:49177227-49250989	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49159400-49181000	Weak transcription	Small Intestine	intestine
2	chr12:49168400-49181400	Weak transcription	Fetal Kidney	kidney
3	chr12:49169800-49181200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:49172200-49181600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:49172400-49181200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:49174600-49181000	Weak transcription	HSMMtube	muscle
7	chr12:49174800-49181200	Weak transcription	Brain Substantia Nigra	brain
8	chr12:49174800-49181200	Weak transcription	HUVEC	blood vessel
9	chr12:49175800-49181600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr12:49176200-49181200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:49176400-49181000	Weak transcription	NHEK	skin
12	chr12:49177000-49181000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr12:49177000-49181000	Weak transcription	NHLF	lung
14	chr12:49177200-49181000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:49177200-49181000	Enhancers	Left Ventricle	heart
16	chr12:49177400-49181000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:49177400-49181000	Weak transcription	Liver	Liver
18	chr12:49177600-49181000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:49178600-49181000	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr12:49178800-49181000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr12:49178800-49181000	Enhancers	Right Ventricle	heart
22	chr12:49179600-49181000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:49179600-49181000	Enhancers	Brain Germinal Matrix	brain
24	chr12:49179600-49181000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr12:49179600-49181600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:49179800-49181000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:49179800-49181000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:49179800-49181000	Enhancers	Aorta	Aorta
29	chr12:49179800-49181000	Enhancers	Ovary	ovary
30	chr12:49179800-49181000	Enhancers	Pancreas	Pancrea
31	chr12:49179800-49181200	Enhancers	NHDF-Ad	bronchial
32	chr12:49179800-49181600	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr12:49180000-49181000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:49180000-49181000	Enhancers	Colonic Mucosa	Colon
35	chr12:49180000-49181000	Enhancers	Fetal Brain Female	brain
36	chr12:49180000-49181600	Enhancers	Lung	lung
37	chr12:49180200-49181000	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr12:49180200-49181200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr12:49180200-49181200	Enhancers	Fetal Muscle Trunk	muscle
40	chr12:49180200-49181400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:49180200-49181800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr12:49180400-49181000	Genic enhancers	Fetal Stomach	stomach
43	chr12:49180400-49181000	Enhancers	HepG2	liver
44	chr12:49180400-49181400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:49180400-49181600	Enhancers	Stomach Mucosa	stomach
46	chr12:49180400-49182000	Enhancers	Spleen	Spleen
47	chr12:49180400-49182200	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr12:49180400-49182400	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr12:49180600-49181000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:49180600-49181000	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links