Variant report

Variant	rs10080254
Chromosome Location	chr6:149275131-149275132
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149067550..149069400-chr6:149273636..149276626,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111962	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10499256	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs17080152	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs17666460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17728703	1.00[CHB][hapmap];0.92[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs17728886	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41288425	1.00[ASN][1000 genomes]
rs9373582	0.80[TSI][hapmap]
rs9390641	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9390643	1.00[CEU][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9498182	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149256600-149292600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:149257000-149285000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:149257600-149276200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:149261400-149285000	Weak transcription	Spleen	Spleen
5	chr6:149262000-149289600	Weak transcription	Aorta	Aorta
6	chr6:149262200-149276200	Weak transcription	Pancreas	Pancrea
7	chr6:149263400-149275400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:149263400-149275600	Weak transcription	Primary B cells from cord blood	blood
9	chr6:149263400-149275600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr6:149263400-149275600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:149266800-149276200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:149267000-149276400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:149269200-149276600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:149269400-149276000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:149269400-149277600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:149269400-149288800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:149269400-149291400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:149269600-149275800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr6:149269600-149276400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:149269600-149277800	Weak transcription	Brain Substantia Nigra	brain
21	chr6:149271200-149275600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:149271200-149276600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:149271200-149288600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:149271400-149275600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr6:149271400-149276000	Weak transcription	Right Atrium	heart
26	chr6:149271600-149275600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr6:149271600-149276000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr6:149271600-149276000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:149271600-149277600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:149271600-149285600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:149271800-149275400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:149271800-149275600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:149271800-149276000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:149272800-149283400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:149273600-149275800	Weak transcription	Fetal Intestine Small	intestine
36	chr6:149273800-149276200	Weak transcription	Stomach Mucosa	stomach
37	chr6:149274000-149276000	Weak transcription	Dnd41	blood
38	chr6:149274000-149277200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:149274000-149286400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:149274000-149288800	Weak transcription	NHEK	skin
41	chr6:149274000-149293800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:149274200-149275600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr6:149274200-149276600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:149274200-149284000	Weak transcription	Ovary	ovary
45	chr6:149274200-149288400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr6:149274200-149288800	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr6:149274400-149276000	Weak transcription	Fetal Stomach	stomach
48	chr6:149274400-149290400	Weak transcription	Fetal Kidney	kidney
49	chr6:149274600-149275600	Weak transcription	Fetal Lung	lung
50	chr6:149274600-149275800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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