Variant report

Variant	rs6674736
Chromosome Location	chr1:171314682-171314683
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	GATA3	chr1:171314483-171315076	SK-N-SH	brain:	n/a	chr1:171314750-171314763
2	NFIC	chr1:171314554-171315014	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr1:171314547-171315027	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr1:171314451-171315054	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr1:171314424-171315084	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr1:171314614-171315110	SK-N-SH	brain:	n/a	chr1:171314750-171314763

Variant related genes	Relation type
TOP1P1	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12065835	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes]
rs12076180	1.00[ASN][1000 genomes]
rs12076444	1.00[ASN][1000 genomes]
rs12119640	0.91[EUR][1000 genomes]
rs12120784	0.91[EUR][1000 genomes]
rs12121703	0.91[EUR][1000 genomes]
rs12122309	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122751	1.00[CHB][hapmap]
rs12130175	0.82[EUR][1000 genomes]
rs12131722	0.82[EUR][1000 genomes]
rs12138802	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12141357	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs12142448	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs12142487	0.91[EUR][1000 genomes]
rs12145368	1.00[CEU][hapmap];0.85[GIH][hapmap]
rs16828330	1.00[ASN][1000 genomes]
rs16864312	1.00[JPT][hapmap]
rs16864314	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16864332	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16864389	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16864392	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16864395	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16864396	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16864417	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16864434	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28360434	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs45542731	1.00[ASN][1000 genomes]
rs60349465	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667529	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6674434	0.91[EUR][1000 genomes]
rs6675911	0.91[EUR][1000 genomes]
rs6685422	1.00[JPT][hapmap]
rs6699241	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6699345	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes]
rs717023	1.00[JPT][hapmap]
rs717024	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7516764	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7518815	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525073	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543159	1.00[JPT][hapmap]
rs7545776	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7548898	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1002423	chr1:171294384-171376936	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv548188	chr1:171308832-171371998	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171305600-171315200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:171312800-171315600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:171313800-171315000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:171313800-171315400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:171313800-171315600	Enhancers	Liver	Liver
6	chr1:171314400-171315000	Weak transcription	Fetal Intestine Small	intestine

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