Variant report

Variant	rs1013902
Chromosome Location	chr6:142719728-142719729
allele	A/G
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	POLR2A	chr6:142719379-142719778	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:104406220..104408356-chr6:142717521..142720116,2	MCF-7	breast:
2	chr6:142709536..142712491-chr6:142719118..142721434,2	K562	blood:
3	chr6:142716545..142718055-chr6:142718448..142720130,2	MCF-7	breast:

Variant related genes	Relation type
GPR126	TF binding region
ENSG00000112414	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs17071798	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2064314	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2143390	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223616	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294765	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2294768	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294770	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2294772	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2294773	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2294774	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34701089	0.86[EUR][1000 genomes]
rs41289839	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6570512	0.88[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6913116	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7758750	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7759268	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9321865	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9321871	0.83[EUR][1000 genomes]
rs9373343	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9373345	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9376687	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9376689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9385993	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9385994	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9389988	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9389990	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9403379	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9403384	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484645	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142698600-142733200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:142708000-142734800	Weak transcription	Esophagus	oesophagus
3	chr6:142709200-142721000	Weak transcription	Fetal Intestine Small	intestine
4	chr6:142710000-142721600	Weak transcription	NHLF	lung
5	chr6:142710200-142733400	Weak transcription	HSMM	muscle
6	chr6:142711400-142725000	Strong transcription	HepG2	liver
7	chr6:142711800-142725200	Strong transcription	Liver	Liver
8	chr6:142712200-142735000	Weak transcription	Fetal Brain Male	brain
9	chr6:142714200-142733200	Weak transcription	HMEC	breast
10	chr6:142717200-142721600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:142717600-142721000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:142717600-142721000	Enhancers	Primary T cells from cord blood	blood
13	chr6:142717600-142721600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:142717600-142721600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr6:142717600-142724600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:142717600-142725800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:142718000-142721600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:142718000-142763200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:142718200-142721600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:142718400-142722400	Strong transcription	Fetal Lung	lung
21	chr6:142718600-142720200	Strong transcription	HUVEC	blood vessel
22	chr6:142718600-142720400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:142718600-142720800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:142718600-142720800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:142718600-142721000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:142718600-142724000	Strong transcription	Placenta	Placenta
27	chr6:142718800-142720600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:142719200-142719800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:142719200-142720600	Enhancers	Duodenum Mucosa	Duodenum
30	chr6:142719200-142722600	Strong transcription	A549	lung
31	chr6:142719400-142719800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:142719600-142719800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr6:142719600-142719800	Enhancers	Small Intestine	intestine
34	chr6:142719600-142720400	Strong transcription	NHEK	skin
35	chr6:142719600-142721000	Weak transcription	Stomach Mucosa	stomach

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