Variant report

Variant	rs62397308
Chromosome Location	chr6:15242075-15242076
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	chr6:15241683-15242156	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:15239185..15241876-chr6:15241948..15244748,3	MCF-7	breast:
2	chr6:15208660..15211196-chr6:15241386..15243147,2	MCF-7	breast:

Variant related genes	Relation type
JARID2	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11751391	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11755759	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11759040	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12193844	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17619730	0.82[ASN][1000 genomes]
rs62397310	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830593	chr6:15049636-15244190	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv830594	chr6:15171158-15261296	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15240000-15243400	Weak transcription	Right Ventricle	heart
2	chr6:15240000-15244400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr6:15240000-15244600	Weak transcription	Left Ventricle	heart
4	chr6:15240000-15244600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:15240000-15244800	Weak transcription	Aorta	Aorta
6	chr6:15240000-15244800	Weak transcription	Right Atrium	heart
7	chr6:15240200-15242200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:15240200-15243600	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:15240200-15244600	Weak transcription	Colon Smooth Muscle	Colon
10	chr6:15240400-15242400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr6:15240400-15242600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:15240400-15243000	Weak transcription	HUVEC	blood vessel
13	chr6:15240400-15244000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:15240400-15244200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:15240400-15244200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:15240400-15244400	Weak transcription	Fetal Brain Female	brain
17	chr6:15240400-15244400	Weak transcription	Fetal Lung	lung
18	chr6:15240400-15244400	Weak transcription	Fetal Stomach	stomach
19	chr6:15240400-15244400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:15240400-15244600	Weak transcription	Brain Substantia Nigra	brain
21	chr6:15240400-15244600	Weak transcription	HSMMtube	muscle
22	chr6:15240600-15242800	Weak transcription	Adipose Nuclei	Adipose
23	chr6:15240600-15244400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:15240600-15244600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:15240600-15244600	Weak transcription	Brain Germinal Matrix	brain
26	chr6:15240600-15244600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:15240600-15244600	Weak transcription	HSMM	muscle
28	chr6:15240600-15244800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:15240800-15242600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:15240800-15242800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr6:15240800-15243600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:15240800-15244200	Weak transcription	Fetal Heart	heart
33	chr6:15241000-15244600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:15241400-15242800	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr6:15241400-15242800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr6:15241400-15242800	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr6:15241400-15242800	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr6:15241600-15243000	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr6:15241800-15242400	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr6:15242000-15242600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:15242000-15243000	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr6:15242000-15243400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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