Variant report

Variant	rs12494997
Chromosome Location	chr3:140791224-140791225
allele	A/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	POLR2A	chr3:140791205-140791270	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:140785419..140788357-chr3:140788951..140791966,3	MCF-7	breast:
2	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	0.92[ASN][1000 genomes]
rs11928846	0.84[CEU][hapmap]
rs1365630	0.93[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs1426962	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]
rs1426963	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[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]
rs1559896	0.84[CEU][hapmap]
rs4683547	0.84[CEU][hapmap]
rs59279694	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6439977	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6793789	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6804474	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7622090	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs890528	0.83[AFR][1000 genomes]
rs919157	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs9817298	1.00[CEU][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9817591	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9823283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9823690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9842086	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs9844927	0.80[EUR][1000 genomes]
rs9882989	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[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	chr3:140788000-140791400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:140788000-140793000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:140788200-140791800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:140788200-140797200	Enhancers	H9 Cell Line	embryonic stem cell
10	chr3:140788600-140795000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:140788800-140791600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr3:140789000-140797600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr3:140789400-140791400	Enhancers	Brain Germinal Matrix	brain
14	chr3:140789400-140795800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:140789600-140791400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:140789600-140791400	Genic enhancers	Fetal Muscle Leg	muscle
17	chr3:140789600-140791800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr3:140789600-140798000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:140789800-140791400	Genic enhancers	Fetal Muscle Trunk	muscle
20	chr3:140790200-140795400	Weak transcription	Fetal Intestine Small	intestine
21	chr3:140790400-140791800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
22	chr3:140790600-140791600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
23	chr3:140790600-140791800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
24	chr3:140790600-140792000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:140790600-140795000	Weak transcription	Fetal Brain Male	brain
26	chr3:140790600-140795200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:140790600-140802800	Weak transcription	Dnd41	blood
28	chr3:140790800-140791400	Enhancers	Right Ventricle	heart
29	chr3:140790800-140795400	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr3:140790800-140795400	Weak transcription	Right Atrium	heart
31	chr3:140791000-140791400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:140791000-140791400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
33	chr3:140791000-140792400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:140791000-140794600	Weak transcription	Fetal Stomach	stomach
35	chr3:140791000-140795000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:140791200-140792400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:140791200-140792400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:140791200-140792400	Weak transcription	Fetal Lung	lung
39	chr3:140791200-140792400	Weak transcription	Pancreas	Pancrea
40	chr3:140791200-140792600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:140791200-140792600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:140791200-140793800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr3:140791200-140796400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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