Variant report

Variant	rs1426962
Chromosome Location	chr3:140790847-140790848
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	chr3:140790604-140790926	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:140785419..140788357-chr3:140788951..140791966,3	MCF-7	breast:
2	chr3:140789496..140791213-chr3:140794078..140795843,2	K562	blood:
3	chr3:140789863..140792661-chr3:140847892..140850124,2	MCF-7	breast:

Variant related genes	Relation type
SPSB4	TF binding region
ENSG00000175093	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10935417	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11928846	0.84[CEU][hapmap]
rs12494997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1365630	0.93[CEU][hapmap];0.86[CHB][hapmap]
rs1426963	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1559896	0.84[CEU][hapmap]
rs4683547	0.84[CEU][hapmap]
rs59279694	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6439977	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6771494	0.83[AFR][1000 genomes]
rs6793789	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6804474	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7622090	1.00[CEU][hapmap];0.82[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs890528	0.90[AFR][1000 genomes]
rs919157	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9817298	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9817591	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9823283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9823690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9842086	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs9882989	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140777400-140795000	Weak transcription	Fetal Brain Female	brain
2	chr3:140783600-140794200	Weak transcription	Fetal Kidney	kidney
3	chr3:140785800-140795000	Enhancers	Fetal Heart	heart
4	chr3:140785800-140795000	Weak transcription	Lung	lung
5	chr3:140786200-140794000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:140787800-140791200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:140788000-140791400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:140788000-140793000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:140788200-140791800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:140788200-140797200	Enhancers	H9 Cell Line	embryonic stem cell
11	chr3:140788600-140795000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:140788800-140791200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:140788800-140791600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr3:140789000-140797600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr3:140789200-140791000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:140789400-140791400	Enhancers	Brain Germinal Matrix	brain
17	chr3:140789400-140795800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr3:140789600-140791200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:140789600-140791400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:140789600-140791400	Genic enhancers	Fetal Muscle Leg	muscle
21	chr3:140789600-140791800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:140789600-140798000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:140789800-140791000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr3:140789800-140791200	Enhancers	Fetal Lung	lung
25	chr3:140789800-140791200	Enhancers	Pancreas	Pancrea
26	chr3:140789800-140791400	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr3:140790000-140791200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr3:140790200-140791000	Genic enhancers	Fetal Stomach	stomach
29	chr3:140790200-140795400	Weak transcription	Fetal Intestine Small	intestine
30	chr3:140790400-140791000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:140790400-140791200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:140790400-140791800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
33	chr3:140790600-140791200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:140790600-140791600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
35	chr3:140790600-140791800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
36	chr3:140790600-140792000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:140790600-140795000	Weak transcription	Fetal Brain Male	brain
38	chr3:140790600-140795200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:140790600-140802800	Weak transcription	Dnd41	blood
40	chr3:140790800-140791000	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr3:140790800-140791400	Enhancers	Right Ventricle	heart
42	chr3:140790800-140795400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr3:140790800-140795400	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links