Variant report

Variant	rs3985808
Chromosome Location	chr15:52219990-52219991
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	chr15:52219958-52220533	K562	blood:	n/a	n/a
2	POLR2A	chr15:52219292-52220101	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52215264..52217521-chr15:52219809..52221675,2	K562	blood:
2	chr15:52215248..52218294-chr15:52218461..52220476,3	K562	blood:
3	chr15:52219989..52222508-chr15:52224488..52226583,2	MCF-7	breast:

Variant related genes	Relation type
TMOD3	TF binding region
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2198804	1.00[AMR][1000 genomes]
rs28416491	0.90[ASN][1000 genomes]
rs2959281	0.86[JPT][hapmap]
rs3751593	1.00[AMR][1000 genomes]
rs3803365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs56903771	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs57897477	1.00[AMR][1000 genomes]
rs58370000	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs58471786	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58601413	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59784585	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60409555	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60700084	1.00[AMR][1000 genomes];0.96[ASN][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	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52179600-52259800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:52181200-52221000	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr15:52183200-52223000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:52191000-52222800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:52193400-52227800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:52193400-52232800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:52193600-52233600	Weak transcription	Fetal Brain Male	brain
8	chr15:52194200-52228200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:52194200-52231600	Weak transcription	Psoas Muscle	Psoas
10	chr15:52194400-52236800	Weak transcription	Fetal Kidney	kidney
11	chr15:52194400-52239000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:52196200-52234000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:52197000-52234200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr15:52197000-52234800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:52200400-52220800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:52200400-52262200	Weak transcription	Stomach Mucosa	stomach
17	chr15:52201000-52238800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr15:52201800-52223000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr15:52202000-52230000	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:52204600-52224600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:52204800-52238800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr15:52208000-52222800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:52210000-52233600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr15:52210000-52239000	Weak transcription	Colon Smooth Muscle	Colon
25	chr15:52210200-52224200	Strong transcription	A549	lung
26	chr15:52211200-52230400	Weak transcription	K562	blood
27	chr15:52211600-52228800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:52211600-52237600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr15:52211600-52239200	Weak transcription	Right Ventricle	heart
30	chr15:52212400-52241600	Weak transcription	Small Intestine	intestine
31	chr15:52212800-52221000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:52213000-52223400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:52214000-52226200	Weak transcription	Ovary	ovary
34	chr15:52215200-52223000	Weak transcription	NHDF-Ad	bronchial
35	chr15:52215200-52234000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr15:52215400-52223000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr15:52215400-52223000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:52215800-52226200	Weak transcription	Fetal Brain Female	brain
39	chr15:52216000-52223000	Weak transcription	HepG2	liver
40	chr15:52216000-52229600	Weak transcription	Colonic Mucosa	Colon
41	chr15:52216000-52238600	Weak transcription	Pancreas	Pancrea
42	chr15:52216200-52227400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:52216400-52229600	Weak transcription	HSMMtube	muscle
44	chr15:52216400-52234200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:52216800-52222800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr15:52217000-52222600	Weak transcription	Hela-S3	cervix
47	chr15:52217000-52223800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr15:52217000-52227200	Weak transcription	Brain Germinal Matrix	brain
49	chr15:52217000-52231600	Weak transcription	Brain Hippocampus Middle	brain
50	chr15:52217200-52226600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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