Variant report

Variant	rs59729812
Chromosome Location	chr1:9882666-9882667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:9881352..9884024-chr1:9922177..9924275,2	K562	blood:
2	chr1:9775370..9777474-chr1:9882453..9884913,2	MCF-7	breast:
3	chr1:9875644..9877842-chr1:9881714..9883858,3	MCF-7	breast:
4	chr1:9881290..9883388-chr1:9900739..9903390,2	MCF-7	breast:
5	chr1:9881807..9884566-chr1:10002965..10004897,2	K562	blood:
6	chr1:9881807..9884566-chr1:10002290..10004897,3	K562	blood:
7	chr1:9882289..9884339-chr1:9907801..9910859,3	K562	blood:
8	chr1:9882501..9887964-chr1:9906388..9911794,10	MCF-7	breast:
9	chr1:9882661..9885013-chr1:10458252..10460185,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228150	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000173614	Chromatin interaction
ENSG00000223989	Chromatin interaction
ENSG00000171608	Chromatin interaction
ENSG00000142657	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10779731	0.89[EUR][1000 genomes]
rs10864437	0.91[EUR][1000 genomes]
rs10864438	0.89[EUR][1000 genomes]
rs11121490	0.83[EUR][1000 genomes]
rs11121493	0.85[EUR][1000 genomes]
rs11674	0.89[EUR][1000 genomes]
rs11806520	0.93[EUR][1000 genomes]
rs12034239	0.82[EUR][1000 genomes]
rs12047054	0.88[EUR][1000 genomes]
rs12068489	0.90[ASN][1000 genomes]
rs12078414	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12087051	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12088273	0.91[EUR][1000 genomes]
rs1220386	0.84[ASN][1000 genomes]
rs1228434	0.85[EUR][1000 genomes]
rs1615629	0.95[EUR][1000 genomes]
rs1631962	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1660738	0.91[ASN][1000 genomes]
rs1660741	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1660742	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1767277	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2582979	0.91[ASN][1000 genomes]
rs2788605	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4585981	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56109009	0.89[EUR][1000 genomes]
rs57480158	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57560942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6699320	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72855716	0.89[EUR][1000 genomes]
rs72855733	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72855735	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72855745	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72855747	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7550246	0.89[EUR][1000 genomes]
rs767762	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935071	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs946277	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs946278	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs946279	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv3330047	chr1:9882590-9885538	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9869800-9882800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:9873600-9883000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:9880200-9884400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:9880800-9882800	Weak transcription	Pancreas	Pancrea
5	chr1:9880800-9883000	Flanking Active TSS	Dnd41	blood
6	chr1:9881000-9882800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:9881200-9884400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:9881400-9882800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:9881400-9883000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:9881800-9882800	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr1:9881800-9883000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:9881800-9884400	Active TSS	NHEK	skin
13	chr1:9881800-9884800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:9881800-9884800	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr1:9882000-9882800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:9882000-9882800	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr1:9882000-9882800	Flanking Active TSS	A549	lung
18	chr1:9882000-9882800	Flanking Active TSS	NH-A	brain
19	chr1:9882000-9883000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr1:9882000-9883000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr1:9882000-9883000	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr1:9882000-9883000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr1:9882000-9883200	Flanking Active TSS	Fetal Brain Male	brain
24	chr1:9882000-9883400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr1:9882000-9884400	Active TSS	HMEC	breast
26	chr1:9882000-9884600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:9882200-9882800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr1:9882200-9882800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:9882200-9882800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr1:9882200-9882800	Flanking Active TSS	Hela-S3	cervix
31	chr1:9882200-9883000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr1:9882200-9883000	Flanking Active TSS	Osteobl	bone
33	chr1:9882200-9883200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:9882200-9883200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:9882200-9883200	Flanking Active TSS	Fetal Muscle Leg	muscle
36	chr1:9882200-9883400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:9882200-9883400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:9882200-9883400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:9882200-9883600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:9882200-9884400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:9882400-9882800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr1:9882400-9882800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
43	chr1:9882400-9882800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
44	chr1:9882400-9882800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:9882400-9882800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:9882400-9882800	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr1:9882400-9882800	Flanking Active TSS	Fetal Intestine Small	intestine
48	chr1:9882400-9882800	Flanking Active TSS	Fetal Kidney	kidney
49	chr1:9882400-9882800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr1:9882400-9882800	Flanking Active TSS	Fetal Stomach	stomach

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