Variant report

Variant	rs12908852
Chromosome Location	chr15:93192039-93192040
allele	C/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	chr15:93191783-93192321	T-47D	breast:	n/a	n/a
2	GATA3	chr15:93191456-93192374	MCF-7	breast:	n/a	n/a
3	GATA3	chr15:93191893-93192200	MCF-7	breast:	n/a	n/a
4	GATA2	chr15:93191905-93192129	SH-SY5Y	brain:	n/a	n/a
5	FOXA1	chr15:93191892-93192100	T-47D	breast:	n/a	n/a
6	GATA3	chr15:93191815-93192318	T-47D	breast:	n/a	n/a
7	NR2F2	chr15:93191346-93192238	MCF-7	breast:	n/a	chr15:93191581-93191596

No.	Distal block	Cell Line	Cell type
1	chr15:93191617..93195403-chr15:93257490..93261490,4	MCF-7	breast:
2	chr15:93191674..93195100-chr15:93197023..93199781,4	K562	blood:
3	chr15:93191935..93193654-chr15:93222060..93224471,2	MCF-7	breast:
4	chr15:93191674..93194202-chr15:93197134..93199781,2	K562	blood:

Variant related genes	Relation type
FAM174B	TF binding region
ENSG00000185442	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12443091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496712	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16974307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs184048	0.80[EUR][1000 genomes]
rs2254142	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs2453901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285754	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs285755	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs285757	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs285758	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs285766	0.80[EUR][1000 genomes]
rs285772	0.96[EUR][1000 genomes]
rs366789	0.82[EUR][1000 genomes]
rs373481	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs406032	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413450	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434826	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs503112	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6496969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178546	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
5	nsv1040501	chr15:93177153-93286393	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12908852	LOC400451	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93171000-93197400	Weak transcription	Primary T cells from cord blood	blood
2	chr15:93182000-93197800	Weak transcription	Small Intestine	intestine
3	chr15:93182600-93197200	Weak transcription	Fetal Kidney	kidney
4	chr15:93183200-93198400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:93186400-93194200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:93186800-93192800	Enhancers	HUVEC	blood vessel
7	chr15:93187200-93193000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:93187400-93193200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr15:93187400-93194000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:93187400-93194000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr15:93187600-93195800	Weak transcription	Brain Angular Gyrus	brain
12	chr15:93187800-93195600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr15:93188200-93192200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:93188200-93193000	Enhancers	H9 Cell Line	embryonic stem cell
15	chr15:93188400-93192400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr15:93188400-93192400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:93189000-93193400	Weak transcription	Fetal Stomach	stomach
18	chr15:93189000-93194000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr15:93189000-93195600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr15:93189000-93197000	Weak transcription	Brain Hippocampus Middle	brain
21	chr15:93189200-93195200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:93189200-93195400	Weak transcription	Right Ventricle	heart
23	chr15:93189400-93193600	Weak transcription	Fetal Lung	lung
24	chr15:93189400-93193600	Weak transcription	Placenta	Placenta
25	chr15:93189400-93194000	Weak transcription	Fetal Muscle Leg	muscle
26	chr15:93189400-93197000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:93189400-93197000	Weak transcription	Esophagus	oesophagus
28	chr15:93189800-93193000	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr15:93190400-93192200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:93190400-93194200	Enhancers	Gastric	stomach
31	chr15:93190600-93197000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr15:93190800-93194000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr15:93190800-93195400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:93191000-93192400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:93191000-93193600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:93191000-93194000	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr15:93191000-93194200	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr15:93191000-93196600	Weak transcription	HSMM	muscle
39	chr15:93191000-93197400	Weak transcription	HSMMtube	muscle
40	chr15:93191200-93192200	Enhancers	Stomach Smooth Muscle	stomach
41	chr15:93191400-93194200	Enhancers	Pancreas	Pancrea
42	chr15:93191600-93193200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr15:93191800-93192200	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr15:93191800-93193400	Weak transcription	GM12878-XiMat	blood
45	chr15:93191800-93194200	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr15:93191800-93195400	Weak transcription	Fetal Intestine Small	intestine
47	chr15:93192000-93192600	Enhancers	Stomach Mucosa	stomach
48	chr15:93192000-93193600	Weak transcription	Left Ventricle	heart
49	chr15:93192000-93193600	Weak transcription	Lung	lung
50	chr15:93192000-93193800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links