Variant report

Variant	rs12509289
Chromosome Location	chr4:30839290-30839291
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10025293	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10027054	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10517216	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs11721555	0.82[JPT][hapmap]
rs11946238	0.88[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12513276	0.86[EUR][1000 genomes]
rs13135261	0.81[JPT][hapmap]
rs13145415	0.86[CEU][hapmap]
rs1345147	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1374650	0.87[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1374651	0.80[ASN][1000 genomes]
rs1374652	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1374654	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1447371	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884042	0.82[JPT][hapmap]
rs16884163	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1823196	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1823197	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1900571	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121656	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2121659	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs34211313	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6810526	0.81[JPT][hapmap]
rs6811850	0.81[JPT][hapmap]
rs6819990	0.81[JPT][hapmap]
rs6842641	0.85[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6842866	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844742	0.86[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7682792	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs958274	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878810	chr4:30823157-30987395	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv998450	chr4:30823631-31628179	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:30833400-30842800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr4:30835200-30842800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr4:30836600-30842400	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr4:30837000-30839400	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr4:30837200-30841600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:30837200-30841600	Weak transcription	Aorta	Aorta
7	chr4:30837200-30841800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:30837200-30841800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:30837200-30843400	Enhancers	Hela-S3	cervix
10	chr4:30837400-30841200	Weak transcription	Right Ventricle	heart
11	chr4:30837800-30840200	Enhancers	NH-A	brain
12	chr4:30838000-30840600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:30838000-30840600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr4:30838200-30840800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr4:30838400-30840200	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr4:30838400-30840400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:30838400-30840400	Enhancers	Fetal Stomach	stomach
18	chr4:30838400-30840600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:30838400-30840800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:30838600-30839400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr4:30838600-30839400	Flanking Active TSS	Fetal Heart	heart
22	chr4:30838600-30839400	Enhancers	HSMMtube	muscle
23	chr4:30838600-30840600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:30838600-30840600	Enhancers	Fetal Lung	lung
25	chr4:30838800-30840200	Enhancers	Fetal Brain Male	brain
26	chr4:30838800-30848600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:30839000-30839600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:30839000-30841200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:30839000-30841200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr4:30839000-30841600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr4:30839000-30842000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:30839200-30839600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:30839200-30839600	Weak transcription	Fetal Muscle Leg	muscle
34	chr4:30839200-30841000	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:30839200-30841200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr4:30839200-30841600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:30839200-30848600	Weak transcription	Stomach Smooth Muscle	stomach

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