Variant report

Variant	rs9858204
Chromosome Location	chr3:142299855-142299856
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	CTCF	chr3:142299720-142299870	GM12875	blood:	n/a	n/a
2	TEAD4	chr3:142299851-142300195	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:142296149..142300233-chr3:142313670..142315817,6	K562	blood:
2	chr3:142294568..142300006-chr3:142310942..142319455,13	MCF-7	breast:
3	chr3:142296202..142300183-chr3:142719946..142722583,4	K562	blood:
4	chr3:142294183..142301262-chr3:142311308..142318922,13	MCF-7	breast:

Variant related genes	Relation type
ATR	TF binding region
ENSG00000268129	Chromatin interaction
ENSG00000163714	Chromatin interaction
ENSG00000120756	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10935464	0.90[EUR][1000 genomes]
rs11709758	0.80[JPT][hapmap]
rs11711164	0.88[CHD][hapmap];0.86[GIH][hapmap]
rs11714244	0.80[JPT][hapmap]
rs11719737	0.87[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap]
rs11720007	0.88[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap]
rs11720762	0.80[JPT][hapmap]
rs13316756	0.86[ASN][1000 genomes]
rs17623058	0.81[CEU][hapmap]
rs2140433	0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2140434	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2177397	0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2229032	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs2291363	0.88[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap]
rs2306700	0.87[CHD][hapmap];0.87[GIH][hapmap];0.80[JPT][hapmap]
rs28365824	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28378300	0.84[ASN][1000 genomes]
rs28647471	0.87[ASN][1000 genomes]
rs28709617	0.87[ASN][1000 genomes]
rs3922731	0.89[EUR][1000 genomes]
rs4398471	0.88[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4582093	0.86[ASN][1000 genomes]
rs55994893	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56383228	0.87[ASN][1000 genomes]
rs56397702	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58910647	0.86[ASN][1000 genomes]
rs60001529	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6440095	0.89[ASN][1000 genomes]
rs6440096	0.88[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6440097	0.87[ASN][1000 genomes]
rs66597875	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6778383	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73228757	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73228758	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73238195	0.84[EUR][1000 genomes]
rs73238200	0.90[EUR][1000 genomes]
rs73238202	0.90[EUR][1000 genomes]
rs73240305	0.95[EUR][1000 genomes]
rs73240309	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73240310	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73240314	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73240316	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73240318	0.86[EUR][1000 genomes]
rs73240323	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73240328	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633021	0.87[ASN][1000 genomes]
rs7638338	0.88[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7642634	0.88[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap]
rs7647212	0.88[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs7647497	0.88[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs9813377	0.87[ASN][1000 genomes]
rs9816128	0.87[ASN][1000 genomes]
rs9816275	0.87[ASN][1000 genomes]
rs9826463	0.87[ASN][1000 genomes]
rs9847445	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs9857567	0.86[ASN][1000 genomes]
rs9862686	0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs9868309	0.88[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142298200-142300400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:142298200-142301800	Weak transcription	Left Ventricle	heart
3	chr3:142298200-142314400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:142298400-142300000	Weak transcription	Placenta	Placenta
5	chr3:142298400-142306000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:142298600-142300200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:142298600-142300400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:142298600-142314400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:142298800-142300200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:142298800-142305600	Weak transcription	Liver	Liver
11	chr3:142298800-142305600	Weak transcription	A549	lung
12	chr3:142299000-142300200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:142299000-142303000	Weak transcription	K562	blood
14	chr3:142299800-142300200	Active TSS	HepG2	liver
15	chr3:142299800-142300800	Enhancers	HUES6 Cell Line	embryonic stem cell

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