Variant report

Variant	rs9496357
Chromosome Location	chr6:142698839-142698840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:142623095..142627464-chr6:142695015..142699315,6	MCF-7	breast:
2	chr6:142697707..142700330-chr6:142702224..142704168,2	MCF-7	breast:
3	chr6:142644594..142647193-chr6:142697392..142699700,4	MCF-7	breast:
4	chr1:151485360..151486235-chr6:142698194..142698929,2	HCT-116	colon:
5	chr6:142696462..142698436-chr6:142698561..142701397,2	MCF-7	breast:
6	chr6:142692998..142695094-chr6:142697780..142699490,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112414	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10080722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10080956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9321867	0.84[ASW][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484631	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484632	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9484633	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496354	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496356	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496358	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496360	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496361	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496365	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496367	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496368	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496371	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9496372	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][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:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142693200-142700000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:142693200-142700200	Enhancers	HMEC	breast
3	chr6:142693200-142700600	Enhancers	Hela-S3	cervix
4	chr6:142694000-142699600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:142694800-142699200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:142695400-142699800	Enhancers	HSMM	muscle
7	chr6:142695600-142700400	Enhancers	Fetal Lung	lung
8	chr6:142695800-142699600	Weak transcription	Fetal Stomach	stomach
9	chr6:142696000-142699200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:142696000-142700200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:142696000-142700200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:142696600-142699600	Enhancers	Fetal Intestine Large	intestine
13	chr6:142696600-142700000	Enhancers	Osteobl	bone
14	chr6:142696800-142699000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:142696800-142699000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:142696800-142699200	Weak transcription	Fetal Heart	heart
17	chr6:142696800-142699400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:142696800-142699400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:142697000-142699200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:142697000-142703200	Weak transcription	NHDF-Ad	bronchial
21	chr6:142697400-142699800	Enhancers	Fetal Intestine Small	intestine
22	chr6:142697600-142699200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:142697600-142699200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:142697600-142699200	Enhancers	HUVEC	blood vessel
25	chr6:142698000-142699000	Flanking Active TSS	NHEK	skin
26	chr6:142698000-142699800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:142698000-142700000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr6:142698000-142700000	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr6:142698000-142700000	Flanking Active TSS	A549	lung
30	chr6:142698000-142700000	Enhancers	HSMMtube	muscle
31	chr6:142698000-142700200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:142698000-142700200	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr6:142698000-142700200	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr6:142698000-142700200	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr6:142698000-142702000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:142698200-142699000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:142698200-142699200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:142698200-142699400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr6:142698200-142699800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:142698200-142700000	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr6:142698200-142700000	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr6:142698200-142700400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr6:142698200-142700400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr6:142698200-142700400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:142698200-142700400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr6:142698200-142700400	Enhancers	Small Intestine	intestine
47	chr6:142698200-142702800	Enhancers	Primary hematopoietic stem cells	blood
48	chr6:142698400-142699200	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr6:142698400-142699400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr6:142698400-142699600	Weak transcription	Fetal Kidney	kidney

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