Variant report

Variant	rs9376689
Chromosome Location	chr6:142696501-142696502
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:142696462..142698436-chr6:142698561..142701397,2	MCF-7	breast:
2	chr6:142693095..142695655-chr6:142695797..142698299,2	MCF-7	breast:
3	chr6:142644270..142645921-chr6:142696254..142697871,2	MCF-7	breast:
4	chr6:142623095..142627464-chr6:142695015..142699315,6	MCF-7	breast:
5	chr6:142624220..142625771-chr6:142695392..142697022,2	MCF-7	breast:
6	chr6:142621770..142624085-chr6:142694807..142697859,4	MCF-7	breast:
7	chr6:142683303..142685618-chr6:142695779..142698326,2	MCF-7	breast:
8	chr6:142695789..142698729-chr6:142704783..142708780,4	MCF-7	breast:

No data

Variant related genes	Relation type
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]
rs1013902	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]
rs17071798	0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2064314	0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2143390	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2223616	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294765	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2294768	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2294770	0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2294772	0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2294773	0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2294774	0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34701089	0.86[EUR][1000 genomes]
rs41289839	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4140531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570512	0.88[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6913116	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7758750	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7759268	0.88[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9321865	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9321871	0.83[EUR][1000 genomes]
rs9373343	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9373345	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9376687	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9385993	0.88[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9385994	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9389988	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9389990	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403379	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9403384	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142693200-142696800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:142693200-142700000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:142693200-142700200	Enhancers	HMEC	breast
4	chr6:142693200-142700600	Enhancers	Hela-S3	cervix
5	chr6:142693400-142696600	Enhancers	Fetal Intestine Small	intestine
6	chr6:142694000-142698000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:142694000-142699600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:142694400-142696800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:142694800-142699200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:142695000-142696600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr6:142695000-142698400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:142695200-142696600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr6:142695200-142696600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr6:142695200-142696600	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr6:142695200-142696600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr6:142695200-142696800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:142695200-142696800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:142695200-142696800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:142695200-142696800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:142695400-142697000	Enhancers	NH-A	brain
21	chr6:142695400-142697400	Flanking Active TSS	HepG2	liver
22	chr6:142695400-142698000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr6:142695400-142698200	Weak transcription	Small Intestine	intestine
24	chr6:142695400-142699800	Enhancers	HSMM	muscle
25	chr6:142695600-142697600	Enhancers	Fetal Kidney	kidney
26	chr6:142695600-142700400	Enhancers	Fetal Lung	lung
27	chr6:142695800-142697000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr6:142695800-142699600	Weak transcription	Fetal Stomach	stomach
29	chr6:142696000-142696800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:142696000-142696800	Enhancers	Fetal Heart	heart
31	chr6:142696000-142699200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:142696000-142700200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:142696000-142700200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:142696200-142696600	Flanking Active TSS	Osteobl	bone
35	chr6:142696200-142696800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:142696200-142696800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:142696200-142696800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:142696200-142697000	Flanking Active TSS	Liver	Liver
39	chr6:142696200-142697000	Flanking Active TSS	NHEK	skin
40	chr6:142696200-142697600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:142696200-142697600	Flanking Active TSS	HUVEC	blood vessel
42	chr6:142696200-142698000	Active TSS	A549	lung
43	chr6:142696200-142698200	Enhancers	Duodenum Mucosa	Duodenum
44	chr6:142696200-142698600	Enhancers	NHLF	lung
45	chr6:142696200-142698800	Enhancers	Stomach Mucosa	stomach
46	chr6:142696400-142696600	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr6:142696400-142696600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr6:142696400-142696600	Active TSS	Fetal Intestine Large	intestine
49	chr6:142696400-142696600	Enhancers	NHDF-Ad	bronchial
50	chr6:142696400-142696800	Enhancers	Primary hematopoietic stem cells	blood

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