Variant report

Variant	rs7131984
Chromosome Location	chr12:73004617-73004618
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TPH2-5	chr12:73004458-73005096	NONHSAT029473

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10735969	0.94[CEU][hapmap]
rs10735970	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10748198	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10748202	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10748203	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10784975	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10784978	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10784979	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10879436	0.81[EUR][1000 genomes]
rs10879439	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10879458	0.80[ASN][1000 genomes]
rs10879459	0.81[ASN][1000 genomes]
rs10879460	0.84[ASN][1000 genomes]
rs10879461	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10879462	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10879464	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10879465	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10879466	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10879472	0.91[ASN][1000 genomes]
rs11179264	0.80[CHB][hapmap]
rs11179280	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11179289	0.87[CHB][hapmap]
rs11179290	0.81[CHB][hapmap]
rs11179293	0.83[CHB][hapmap]
rs11179298	0.83[CHB][hapmap]
rs11179302	0.87[CHB][hapmap]
rs11179307	0.87[CHB][hapmap]
rs11179308	0.90[CHB][hapmap]
rs11613768	0.87[CHB][hapmap]
rs12099552	0.87[CHB][hapmap]
rs1214894	0.94[CEU][hapmap];0.82[CHB][hapmap];0.93[EUR][1000 genomes]
rs1214897	0.94[CEU][hapmap];0.82[CHB][hapmap];0.92[EUR][1000 genomes]
rs1214899	0.94[CEU][hapmap];0.82[CHB][hapmap];0.92[EUR][1000 genomes]
rs12582138	0.83[CHB][hapmap]
rs12821081	0.82[CHB][hapmap]
rs1347194	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1347196	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1353160	0.81[EUR][1000 genomes]
rs1389497	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1444606	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1444607	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1560742	0.87[CHB][hapmap]
rs1687265	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs1817885	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1836042	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1836043	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1836044	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1864837	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1864838	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1965318	0.94[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1991751	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2130660	0.81[CHB][hapmap]
rs2367747	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2887071	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs305396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs305402	0.81[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs305403	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35902343	0.83[CHB][hapmap]
rs3782362	0.87[CEU][hapmap]
rs3782366	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3782367	0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3817612	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3843025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852550	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3910234	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3936356	0.83[CHB][hapmap]
rs3952786	0.87[CHB][hapmap]
rs4100196	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41387445	0.84[ASN][1000 genomes]
rs458942	0.88[ASN][1000 genomes]
rs460406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs58509346	0.81[ASN][1000 genomes]
rs58687032	0.81[ASN][1000 genomes]
rs605027	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs626266	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs6582090	0.93[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs6582093	0.82[ASN][1000 genomes]
rs6582094	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6582095	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs683101	0.94[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs7135547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71457035	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723867	0.94[CEU][hapmap];0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7297703	0.87[CHB][hapmap]
rs7299196	0.87[CHB][hapmap]
rs7299984	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7303841	0.87[CHB][hapmap]
rs7308678	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7309263	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7309651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967001	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7969680	1.00[CEU][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7969934	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs963407	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs972421	0.87[CHB][hapmap]
rs996575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422452	chr12:72485933-73175581	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv899257	chr12:72569746-73145896	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1044083	chr12:72647640-73275526	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv469465	chr12:72655925-73259114	Weak transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv559363	chr12:72655925-73259114	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv868884	chr12:72664763-73241518	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv817280	chr12:72820558-73508605	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv899259	chr12:72885554-73011367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv832454	chr12:72940798-73081180	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv1805187	chr12:72949787-73013475	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1054725	chr12:72990553-73062598	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv2758314	chr12:72990707-73251109	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	esv2759908	chr12:72990707-73251109	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv868885	chr12:72998553-73587081	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:73002200-73006000	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr12:73002200-73006800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:73003600-73005600	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr12:73003600-73007800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr12:73003600-73008800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr12:73004000-73005600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr12:73004000-73005800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr12:73004000-73008000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr12:73004200-73005000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:73004200-73005000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:73004200-73005000	Strong transcription	Fetal Intestine Large	intestine
12	chr12:73004200-73005200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:73004200-73005200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:73004200-73005600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr12:73004200-73006200	Enhancers	H9 Cell Line	embryonic stem cell
16	chr12:73004200-73008000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:73004400-73005200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:73004600-73005200	Strong transcription	Ovary	ovary
19	chr12:73004600-73005600	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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