Variant report

Variant	rs4683739
Chromosome Location	chr3:142837361-142837362
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	UBTF	chr3:142837331-142839986	K562	blood:	n/a	n/a
2	POLR2A	chr3:142837303-142839328	K562	blood:	n/a	n/a
3	POLR2A	chr3:142837235-142842973	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:142837327-142842927	GM12891	blood:	n/a	n/a
5	POLR2A	chr3:142836914-142843085	GM12891	blood:	n/a	n/a
6	TRIM28	chr3:142837282-142838506	K562	blood:	n/a	n/a
7	MTA3	chr3:142837353-142839597	GM12878	blood:	n/a	n/a
8	UBTF	chr3:142837118-142840212	K562	blood:	n/a	n/a
9	POLR2A	chr3:142837346-142838912	K562	blood:	n/a	n/a
10	POLR2A	chr3:142836989-142838822	K562	blood:	n/a	n/a
11	ELK1	chr3:142837357-142837491	K562	blood:	n/a	n/a
12	POLR2A	chr3:142837337-142840691	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:142837347-142837684	K562	blood:	n/a	n/a
14	POLR2A	chr3:142837261-142839233	K562	blood:	n/a	n/a
15	NR2F2	chr3:142837242-142838643	K562	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142295506..142297981-chr3:142837321..142839389,2	K562	blood:
2	chr3:142755305..142760138-chr3:142835756..142840820,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000241679	TF binding region
CHST2	TF binding region
ENSG00000175054	Chromatin interaction
ENSG00000163714	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10804685	0.84[EUR][1000 genomes]
rs11707027	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11708528	0.85[EUR][1000 genomes]
rs11713025	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12494086	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16852921	0.90[CEU][hapmap]
rs1979836	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs2280083	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35746477	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3755739	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3755740	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3856698	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3898303	0.91[CHB][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4149494	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683442	0.84[CEU][hapmap]
rs4683445	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683727	0.85[EUR][1000 genomes]
rs4683737	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683738	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440128	0.84[CEU][hapmap]
rs6799460	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs750869	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs750870	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs7640077	0.81[CEU][hapmap];0.91[CHB][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8179934	0.82[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	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv591921	chr3:142762487-142841740	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1007164	chr3:142837004-142891719	Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr3:142831200-142837400	Weak transcription	GM12878-XiMat	blood
2	chr3:142835200-142837600	Enhancers	Fetal Thymus	thymus
3	chr3:142835600-142837400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:142835800-142837600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:142835800-142837600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:142836200-142837400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:142836600-142839200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:142836800-142837400	Enhancers	Dnd41	blood
9	chr3:142836800-142837600	Flanking Active TSS	K562	blood
10	chr3:142837000-142837400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
11	chr3:142837000-142837800	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr3:142837000-142838000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:142837000-142838200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr3:142837000-142840400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
15	chr3:142837200-142837600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr3:142837200-142837600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr3:142837200-142837800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
18	chr3:142837200-142838000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
19	chr3:142837200-142838400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr3:142837200-142840600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell

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