Variant report

Variant	rs1004741
Chromosome Location	chr15:39918556-39918557
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39887137..39895767-chr15:39912868..39924962,20	MCF-7	breast:
2	chr15:39913171..39923947-chr15:39954798..39966806,32	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1004739	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1004740	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633974	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11638500	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11856294	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857927	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16969445	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16969460	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2411312	0.84[EUR][1000 genomes]
rs2412409	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2412410	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412411	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34275067	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35754803	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3784390	0.92[EUR][1000 genomes]
rs4476147	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56722485	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57969006	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58332880	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60884629	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72725045	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39913200-39924000	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr15:39913400-39921000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:39913400-39922400	Enhancers	Fetal Intestine Large	intestine
4	chr15:39913400-39923800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:39914000-39922800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:39914200-39922600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr15:39914600-39922800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr15:39914600-39923600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr15:39914600-39923600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr15:39914600-39923800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr15:39914800-39923800	Enhancers	Primary T cells fromperipheralblood	blood
12	chr15:39915400-39918800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr15:39915800-39918800	Enhancers	HUVEC	blood vessel
14	chr15:39916000-39918600	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr15:39916000-39918800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:39916000-39920000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr15:39916000-39922200	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr15:39916000-39924000	Enhancers	HMEC	breast
19	chr15:39916200-39918600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:39916200-39918800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:39916200-39920800	Enhancers	Spleen	Spleen
22	chr15:39916200-39921000	Weak transcription	Thymus	Thymus
23	chr15:39916200-39922200	Enhancers	Left Ventricle	heart
24	chr15:39916200-39923400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:39916400-39918600	Enhancers	NHEK	skin
26	chr15:39916400-39918600	Enhancers	NHLF	lung
27	chr15:39916400-39937800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:39916600-39918600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr15:39916600-39918600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:39916600-39918600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:39916600-39918600	Enhancers	Hela-S3	cervix
32	chr15:39916600-39918800	Enhancers	NHDF-Ad	bronchial
33	chr15:39916600-39919600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:39916600-39921000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:39916800-39921600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:39916800-39921800	Enhancers	Right Ventricle	heart
37	chr15:39917000-39920400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:39917400-39923800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr15:39917600-39918600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:39917600-39919800	Enhancers	Fetal Heart	heart
41	chr15:39917600-39920200	Weak transcription	Aorta	Aorta
42	chr15:39917600-39920400	Weak transcription	Psoas Muscle	Psoas
43	chr15:39917600-39920800	Weak transcription	Colon Smooth Muscle	Colon
44	chr15:39917600-39921000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr15:39917600-39921600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr15:39917600-39926200	Weak transcription	Esophagus	oesophagus
47	chr15:39917800-39920000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:39917800-39920000	Weak transcription	Placenta	Placenta
49	chr15:39917800-39920200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:39917800-39920200	Weak transcription	Liver	Liver

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