Variant report

Variant	rs17476396
Chromosome Location	chr6:134003092-134003093
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	SP1	chr6:134002909-134003414	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr6:134002892-134003290	H1-hESC	embryonic stem cell:	n/a	n/a
3	JUND	chr6:134002815-134003448	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:134002970-134003193	H1-hESC	embryonic stem cell:	n/a	n/a
5	GTF2F1	chr6:134003060-134003253	H1-hESC	embryonic stem cell:	n/a	n/a
6	POU5F1	chr6:134003023-134003438	H1-hESC	embryonic stem cell:	n/a	chr6:134003201-134003215 chr6:134003254-134003265 chr6:134003150-134003164 chr6:134003202-134003216 chr6:134003202-134003216 chr6:134003150-134003164 chr6:134003202-134003216 chr6:134003150-134003164
7	ATF2	chr6:134002906-134003434	H1-hESC	embryonic stem cell:	n/a	n/a
8	HDAC2	chr6:134002990-134003493	H1-hESC	embryonic stem cell:	n/a	chr6:134003190-134003204

Variant related genes	Relation type
FTH1P26	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1000025	0.80[ASN][1000 genomes]
rs10485153	0.89[ASN][1000 genomes]
rs10485154	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12203961	0.82[ASN][1000 genomes]
rs12210532	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[ASN][1000 genomes]
rs12216307	0.83[ASN][1000 genomes]
rs12660662	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12660720	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12660957	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12661599	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12717184	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194152	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13194345	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13196860	0.82[ASN][1000 genomes]
rs13200337	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13203797	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13204047	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13205217	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13219946	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1468052	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1468053	0.97[ASN][1000 genomes]
rs1468054	0.86[ASN][1000 genomes]
rs1476382	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17062752	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17398008	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17398029	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17398113	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17398664	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17399159	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1999756	0.80[ASN][1000 genomes]
rs2069060	0.89[ASN][1000 genomes]
rs2207405	0.83[ASN][1000 genomes]
rs2327380	0.81[ASN][1000 genomes]
rs2327381	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34537042	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35081309	0.93[AMR][1000 genomes]
rs35317124	0.89[ASN][1000 genomes]
rs35439350	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35470523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36055382	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55952233	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59635582	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62427563	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62429310	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6569896	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569898	0.82[ASN][1000 genomes]
rs6569899	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs68054668	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6904690	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6906782	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6917316	0.82[ASN][1000 genomes]
rs6918525	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6918884	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6919211	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6921832	0.91[ASN][1000 genomes]
rs6925029	0.84[ASN][1000 genomes]
rs6926195	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6939216	0.91[ASN][1000 genomes]
rs6941465	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71576327	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs736572	0.81[ASN][1000 genomes]
rs766996	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7739104	0.81[ASN][1000 genomes]
rs7739428	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7739826	0.80[ASN][1000 genomes]
rs7749675	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7767765	0.86[ASN][1000 genomes]
rs9321411	0.85[ASN][1000 genomes]
rs9321412	0.91[ASN][1000 genomes]
rs9493690	0.83[CHB][hapmap];0.87[ASN][1000 genomes]
rs9493692	0.87[ASN][1000 genomes]
rs9493695	0.87[ASN][1000 genomes]
rs9493710	0.91[ASN][1000 genomes]
rs9493712	0.82[ASN][1000 genomes]
rs9493716	0.91[ASN][1000 genomes]
rs9493719	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032687	chr6:133987372-134059728	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1024201	chr6:133987372-134062162	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830812	chr6:133993897-134165407	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17476396	C6orf191	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:134000800-134005800	Enhancers	Fetal Lung	lung
2	chr6:134002200-134004600	Enhancers	H1 Cell Line	embryonic stem cell
3	chr6:134002200-134005400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr6:134002400-134003200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:134002400-134003200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr6:134002400-134003400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:134002400-134003400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:134002400-134004600	Enhancers	Fetal Kidney	kidney
9	chr6:134002400-134005000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr6:134002400-134005400	Enhancers	Fetal Stomach	stomach
11	chr6:134002400-134012800	Weak transcription	Ovary	ovary
12	chr6:134002400-134028600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:134002600-134003800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:134002800-134003200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr6:134002800-134003800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:134002800-134004800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:134003000-134003200	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr6:134003000-134003400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:134003000-134003800	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr6:134003000-134004000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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