Variant report

Variant	rs4775193
Chromosome Location	chr15:59950657-59950658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:59950553-59950743	A549	lung:	n/a	n/a
2	POLR2A	chr15:59950631-59951086	HepG2	liver:	n/a	n/a
3	POLR2A	chr15:59949456-59950789	K562	blood:	n/a	n/a
4	MAFK	chr15:59950514-59950705	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:59680945..59682711-chr15:59948219..59950781,2	MCF-7	breast:
2	chr15:59948214..59950768-chr15:59963899..59966386,2	K562	blood:
3	chr15:59949368..59951651-chr15:60769964..60772749,2	K562	blood:
4	chr15:59945879..59953077-chr15:59978622..59984049,13	K562	blood:
5	chr15:59949843..59951651-chr15:60768775..60771464,2	K562	blood:
6	chr15:59946363..59951356-chr15:59979923..59984049,7	K562	blood:

No data

Variant related genes	Relation type
GTF2A2	TF binding region
ENSG00000259238	Chromatin interaction
ENSG00000128915	Chromatin interaction
ENSG00000238767	Chromatin interaction
ENSG00000245534	Chromatin interaction
ENSG00000140299	Chromatin interaction
ENSG00000227161	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12050786	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12161993	0.86[JPT][hapmap]
rs16941544	0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17236713	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17236734	0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17302448	0.93[CHB][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17302608	0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs28395445	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28418513	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28422085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28437066	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28642859	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28654927	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28883924	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4775192	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775198	0.95[EUR][1000 genomes]
rs6151443	0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap]
rs6151457	1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes]
rs6151492	0.85[EUR][1000 genomes]
rs6151497	1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6151505	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6151522	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6151534	0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6151538	0.95[EUR][1000 genomes]
rs6151540	0.95[EUR][1000 genomes]
rs6151567	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151575	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151591	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7178008	0.84[EUR][1000 genomes]
rs8027421	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8033208	0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8033718	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1824522	chr15:59919844-59987181	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
7	nsv1043693	chr15:59944471-59971500	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59949000-59950800	Active TSS	Placenta	Placenta
2	chr15:59949400-59960200	Weak transcription	Fetal Heart	heart
3	chr15:59949800-59951400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:59949800-59954600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:59949800-59954600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:59949800-59957200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:59949800-59957200	Weak transcription	Spleen	Spleen
8	chr15:59949800-59963400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:59949800-59964000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:59949800-59968000	Weak transcription	Stomach Mucosa	stomach
11	chr15:59949800-59968400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:59949800-59980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:59950000-59963200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:59950200-59950800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:59950200-59950800	Active TSS	Primary T cells from cord blood	blood
16	chr15:59950200-59950800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr15:59950200-59950800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr15:59950200-59950800	Enhancers	Liver	Liver
19	chr15:59950200-59951200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:59950200-59951400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:59950200-59951400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:59950200-59951400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr15:59950200-59951400	Weak transcription	HepG2	liver
24	chr15:59950200-59951400	Weak transcription	HSMM	muscle
25	chr15:59950200-59951400	Weak transcription	HUVEC	blood vessel
26	chr15:59950200-59951400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr15:59950200-59951400	Weak transcription	NHDF-Ad	bronchial
28	chr15:59950200-59951600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:59950200-59951600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:59950200-59951600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:59950200-59951800	Weak transcription	GM12878-XiMat	blood
32	chr15:59950200-59952000	Weak transcription	Hela-S3	cervix
33	chr15:59950200-59952200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr15:59950200-59952200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:59950200-59952200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:59950200-59952200	Weak transcription	Fetal Kidney	kidney
37	chr15:59950200-59952200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr15:59950200-59952200	Weak transcription	K562	blood
39	chr15:59950200-59952200	Weak transcription	NHLF	lung
40	chr15:59950200-59952400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:59950200-59952400	Weak transcription	HMEC	breast
42	chr15:59950200-59952400	Weak transcription	NH-A	brain
43	chr15:59950200-59952400	Weak transcription	Osteobl	bone
44	chr15:59950200-59952600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:59950200-59953000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr15:59950200-59953000	Weak transcription	HSMMtube	muscle
47	chr15:59950200-59954200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr15:59950200-59954200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:59950200-59954400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr15:59950200-59954400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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