Variant report

Variant	rs17223130
Chromosome Location	chr12:64716896-64716897
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64715656..64718210-chr12:64724024..64727796,3	K562	blood:
2	chr12:64715951..64718419-chr12:64728633..64731253,2	MCF-7	breast:
3	chr12:64713435..64716211-chr12:64716690..64718444,2	K562	blood:
4	chr12:64715656..64718159-chr12:64726296..64727850,2	K562	blood:

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1002392	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.85[ASN][1000 genomes]
rs10735919	0.82[ASN][1000 genomes]
rs10748005	0.85[ASN][1000 genomes]
rs10748006	0.84[ASN][1000 genomes]
rs10784389	0.81[ASN][1000 genomes]
rs10784390	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10784392	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10784394	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10784397	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10784398	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10784400	0.82[ASN][1000 genomes]
rs10878128	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10878129	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10878130	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10878131	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10878132	0.85[ASN][1000 genomes]
rs10878134	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10878135	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10878140	0.91[ASN][1000 genomes]
rs10878141	0.91[ASN][1000 genomes]
rs10878142	0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11175302	0.82[ASN][1000 genomes]
rs11175307	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11175308	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1162974	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1162976	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1162977	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1178702	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1178703	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1185525	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12297747	0.85[ASN][1000 genomes]
rs12298172	0.82[ASN][1000 genomes]
rs12300514	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12300747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12303938	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309193	0.90[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12317146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12321083	0.81[ASN][1000 genomes]
rs12581905	1.00[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[ASN][1000 genomes]
rs1347576	0.88[ASN][1000 genomes]
rs1436362	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1436363	0.90[ASN][1000 genomes]
rs1545098	0.86[ASN][1000 genomes]
rs17223151	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1808129	0.82[ASN][1000 genomes]
rs1865791	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1865797	0.83[ASN][1000 genomes]
rs1865798	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1898220	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1978794	0.82[ASN][1000 genomes]
rs2010889	0.85[ASN][1000 genomes]
rs2010893	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2082950	0.89[ASN][1000 genomes]
rs2164503	0.86[ASN][1000 genomes]
rs2334885	0.80[ASN][1000 genomes]
rs2878281	0.85[ASN][1000 genomes]
rs4076831	0.86[ASN][1000 genomes]
rs4631982	0.82[ASN][1000 genomes]
rs4763009	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4763010	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4763143	0.82[ASN][1000 genomes]
rs4763144	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4763145	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4763146	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4763147	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4763148	0.85[ASN][1000 genomes]
rs4763149	0.85[ASN][1000 genomes]
rs4763150	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs5015816	0.82[ASN][1000 genomes]
rs5015817	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs5015818	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs56160145	0.83[ASN][1000 genomes]
rs59282249	0.81[ASN][1000 genomes]
rs61034000	0.81[ASN][1000 genomes]
rs61931479	0.88[ASN][1000 genomes]
rs6581534	1.00[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[ASN][1000 genomes]
rs7303208	0.86[ASN][1000 genomes]
rs7306905	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs73116187	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7313249	1.00[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7313429	0.82[ASN][1000 genomes]
rs7316630	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7487859	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7954838	0.86[ASN][1000 genomes]
rs7955726	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7956726	0.90[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7962466	0.86[ASN][1000 genomes]
rs7964830	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7969382	0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7971787	0.85[ASN][1000 genomes]
rs7973109	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7975823	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7976659	0.91[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	esv3351487	chr12:64420364-64763950	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv3509287	chr12:64526217-64736995	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3509288	chr12:64526217-64736995	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv469456	chr12:64710719-64749372	Weak transcription Enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv559202	chr12:64710719-64749372	Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17223130	RASSF3	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64712800-64717600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:64712800-64717800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr12:64713000-64717000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:64713000-64717000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:64713000-64717200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:64714600-64717800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:64714800-64717400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:64714800-64717400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:64714800-64717400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:64714800-64717400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:64714800-64718200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:64714800-64724000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:64715000-64738000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:64716200-64719000	Enhancers	HSMMtube	muscle
15	chr12:64716600-64718200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:64716600-64718600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr12:64716800-64718200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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