Variant report

Variant	rs2561426
Chromosome Location	chr6:39153220-39153221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39135502..39137739-chr6:39151644..39154156,2	MCF-7	breast:
2	chr6:39152659..39161573-chr6:39191951..39198831,12	K562	blood:
3	chr6:39152234..39153949-chr6:39194899..39197101,2	K562	blood:
4	chr6:39152812..39154721-chr6:39166329..39169173,2	K562	blood:
5	chr6:39148107..39150094-chr6:39152838..39154749,3	MCF-7	breast:
6	chr6:39152267..39154461-chr6:39165553..39167804,2	K562	blood:
7	chr6:39152522..39154314-chr6:39191338..39193640,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1465569	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2561424	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2561427	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2815096	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs890923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[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	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39139600-39157600	Weak transcription	Ovary	ovary
2	chr6:39145400-39154600	Weak transcription	Gastric	stomach
3	chr6:39146200-39160400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:39146600-39157400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:39147400-39156000	Weak transcription	Small Intestine	intestine
6	chr6:39148600-39157000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:39148800-39154000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:39149000-39153400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:39149000-39168000	Weak transcription	Fetal Kidney	kidney
10	chr6:39149600-39154400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr6:39150000-39158800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:39150200-39155200	Weak transcription	Fetal Thymus	thymus
13	chr6:39150200-39157600	Weak transcription	Spleen	Spleen
14	chr6:39150600-39193800	Genic enhancers	Fetal Intestine Small	intestine
15	chr6:39150800-39156200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:39150800-39158400	Enhancers	Stomach Mucosa	stomach
17	chr6:39151000-39154600	Enhancers	Esophagus	oesophagus
18	chr6:39151000-39156600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:39151000-39157200	Enhancers	Duodenum Mucosa	Duodenum
20	chr6:39151000-39165200	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr6:39151200-39155800	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr6:39151200-39156200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:39151200-39156200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr6:39151200-39156800	Enhancers	Colonic Mucosa	Colon
25	chr6:39151400-39162200	Weak transcription	Thymus	Thymus
26	chr6:39151600-39161000	Strong transcription	Fetal Stomach	stomach
27	chr6:39151800-39155200	Weak transcription	Lung	lung
28	chr6:39152000-39154200	Enhancers	Fetal Intestine Large	intestine
29	chr6:39152200-39153600	Enhancers	HMEC	breast
30	chr6:39152200-39154800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:39152200-39155400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr6:39152400-39153600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:39152400-39153600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:39152400-39153600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:39152400-39153600	Enhancers	K562	blood
36	chr6:39152400-39154000	Genic enhancers	Liver	Liver
37	chr6:39152600-39153400	Enhancers	NHEK	skin
38	chr6:39152800-39153400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr6:39152800-39153600	Enhancers	A549	lung
40	chr6:39152800-39153600	Flanking Active TSS	Hela-S3	cervix
41	chr6:39152800-39154000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr6:39152800-39156200	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr6:39153000-39153400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:39153000-39153400	Enhancers	Pancreas	Pancrea
45	chr6:39153000-39153600	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr6:39153000-39156000	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr6:39153200-39153400	Enhancers	Placenta Amnion	Placenta Amnion
48	chr6:39153200-39156000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr6:39153200-39162000	Genic enhancers	Placenta	Placenta

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