Variant report

Variant	rs349504
Chromosome Location	chr3:140229445-140229446
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	SIN3AK20	chr3:140229322-140229649	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr3:140229331-140229664	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr3:140229286-140229497	A549	lung:	n/a	chr3:140229394-140229407
4	CTBP2	chr3:140229140-140229668	H1-hESC	embryonic stem cell:	n/a	n/a
5	BACH1	chr3:140229182-140229677	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:140229063-140229718	H1-neurons	neurons:	n/a	n/a
7	SIN3AK20	chr3:140229319-140229689	H1-hESC	embryonic stem cell:	n/a	n/a
8	CEBPB	chr3:140229238-140229541	H1-hESC	embryonic stem cell:	n/a	chr3:140229394-140229407
9	MAFK	chr3:140229276-140229638	H1-hESC	embryonic stem cell:	n/a	chr3:140229474-140229494 chr3:140229476-140229492 chr3:140229481-140229490 chr3:140229477-140229491
10	SIN3A	chr3:140229092-140229758	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr3:140229072-140229623	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
CLSTN2-AS1	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs168386	0.84[ASN][1000 genomes]
rs187031	0.95[CEU][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs349502	0.95[CEU][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs349505	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs349507	0.87[CHB][hapmap];0.85[ASN][1000 genomes]
rs349510	0.83[ASN][1000 genomes]
rs349533	0.84[CEU][hapmap];0.87[CHB][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs349534	0.85[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs349536	0.84[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs349542	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs349563	0.95[CEU][hapmap];0.83[CHB][hapmap]
rs524554	0.91[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap]
rs530046	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs563342	0.91[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap]

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	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv591863	chr3:140126067-140274442	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140224400-140247200	Weak transcription	Ovary	ovary
2	chr3:140225000-140236800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:140227400-140230000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:140227400-140230200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr3:140227400-140240800	Weak transcription	HSMMtube	muscle
6	chr3:140227800-140229800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr3:140227800-140229800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:140227800-140230000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:140228000-140229600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:140228000-140229800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr3:140228000-140230200	Enhancers	H9 Cell Line	embryonic stem cell
12	chr3:140228200-140229600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:140228200-140229600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:140228200-140230000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:140228200-140230000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:140228600-140230400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:140229000-140230000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr3:140229400-140229600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr3:140229400-140229600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr3:140229400-140229600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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