Variant report

Variant	rs6686001
Chromosome Location	chr1:161205898-161205899
allele	G/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	EP300	chr1:161205864-161206369	T-47D	breast:	n/a	n/a
2	FOXA1	chr1:161205832-161206323	T-47D	breast:	n/a	n/a
3	GATA3	chr1:161205819-161206426	T-47D	breast:	n/a	n/a
4	POLR2A	chr1:161205376-161206267	MCF10A-Er-Src	breast:	n/a	n/a
5	FOXA1	chr1:161205829-161206369	T-47D	breast:	n/a	n/a
6	GATA3	chr1:161205846-161206399	T-47D	breast:	n/a	n/a
7	EP300	chr1:161205840-161206390	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161187686..161190489-chr1:161204186..161207080,2	K562	blood:

Variant related genes	Relation type
NR1I3	TF binding region
ENSG00000268387	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11265571	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11584174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12029543	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12030706	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12032041	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12041050	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12565792	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12721035	0.82[JPT][hapmap]
rs16832733	0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs28470413	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28559311	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4077629	1.00[YRI][hapmap]
rs4609448	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656998	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656999	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55802895	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56835010	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6413453	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs72714938	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7532292	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161196400-161207800	Weak transcription	Small Intestine	intestine
2	chr1:161198800-161208200	Weak transcription	NHDF-Ad	bronchial
3	chr1:161199800-161208000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:161199800-161208000	Weak transcription	Hela-S3	cervix
5	chr1:161199800-161211600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:161200200-161207400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:161200200-161208000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:161200400-161212000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:161200600-161208000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:161200600-161211400	Weak transcription	K562	blood
11	chr1:161200800-161206200	Weak transcription	Brain Anterior Caudate	brain
12	chr1:161200800-161206200	Weak transcription	Gastric	stomach
13	chr1:161200800-161207800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:161200800-161208000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:161200800-161208200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:161200800-161211600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:161200800-161214000	Weak transcription	Esophagus	oesophagus
18	chr1:161201000-161211800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:161201200-161206400	Weak transcription	HepG2	liver
20	chr1:161201200-161211800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:161203000-161206800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:161203200-161207600	Weak transcription	Fetal Intestine Large	intestine
23	chr1:161203400-161206800	Weak transcription	Fetal Intestine Small	intestine
24	chr1:161204400-161207200	Enhancers	Placenta	Placenta
25	chr1:161205600-161206000	Transcr. at gene 5' and 3'	Liver	Liver
26	chr1:161205600-161206400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:161205800-161206000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:161205800-161206400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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