Variant report

Variant	rs72859504
Chromosome Location	chr1:10006071-10006072
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:10005475-10006191	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:9968743..9971464-chr1:10005230..10007264,2	MCF-7	breast:
2	chr1:10002451..10004704-chr1:10005139..10006714,2	MCF-7	breast:
3	chr1:10002125..10006916-chr1:10090169..10095056,10	K562	blood:
4	chr1:10001502..10006445-chr1:10090966..10096976,9	MCF-7	breast:
5	chr1:9969022..9974825-chr1:10002123..10006220,12	K562	blood:
6	chr1:9968043..9973723-chr1:10001891..10008599,10	K562	blood:
7	chr1:9946281..9947867-chr1:10004858..10007220,2	K562	blood:

No data

Variant related genes	Relation type
LZIC	TF binding region
RN7SKP269	TF binding region
ENSG00000130939	Chromatin interaction
ENSG00000178585	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000173614	Chromatin interaction
ENSG00000228150	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs56984132	1.00[AMR][1000 genomes]
rs57307308	1.00[AMR][1000 genomes]
rs57906726	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58342183	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72858082	1.00[AMR][1000 genomes]
rs72858083	1.00[AMR][1000 genomes]
rs72858084	1.00[AMR][1000 genomes]
rs72858085	1.00[AMR][1000 genomes]
rs72858093	1.00[AMR][1000 genomes]
rs72858100	1.00[AMR][1000 genomes]
rs72859506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72859548	1.00[AFR][1000 genomes]
rs72859550	1.00[AFR][1000 genomes]
rs72859554	1.00[AFR][1000 genomes]
rs72859555	1.00[AFR][1000 genomes]
rs72859562	1.00[AFR][1000 genomes]
rs72859572	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	nsv1005461	chr1:9972921-10038862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
10	nsv534855	chr1:9972921-10038862	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
11	nsv947175	chr1:9996275-10009860	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10004000-10010600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:10004000-10010600	Weak transcription	Fetal Heart	heart
3	chr1:10004000-10034000	Weak transcription	Aorta	Aorta
4	chr1:10004200-10007000	Weak transcription	Fetal Stomach	stomach
5	chr1:10004200-10007200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:10004200-10010000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:10004200-10010400	Weak transcription	Fetal Lung	lung
8	chr1:10004200-10010600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:10004200-10010600	Weak transcription	Fetal Brain Male	brain
10	chr1:10004200-10010600	Weak transcription	Fetal Kidney	kidney
11	chr1:10004200-10010600	Weak transcription	Ovary	ovary
12	chr1:10004200-10011000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:10004200-10019400	Weak transcription	NH-A	brain
14	chr1:10004200-10021000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:10004200-10033800	Weak transcription	Gastric	stomach
16	chr1:10004400-10007200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:10004400-10007400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:10004400-10009200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:10004400-10010000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:10004400-10010000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:10004400-10010000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:10004400-10010000	Weak transcription	Stomach Mucosa	stomach
23	chr1:10004400-10010200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:10004400-10010200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:10004400-10010200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:10004400-10010200	Weak transcription	Placenta	Placenta
27	chr1:10004400-10010400	Weak transcription	Esophagus	oesophagus
28	chr1:10004400-10010600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:10004400-10010600	Weak transcription	Brain Angular Gyrus	brain
30	chr1:10004400-10010600	Weak transcription	Fetal Brain Female	brain
31	chr1:10004400-10010600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:10004400-10010800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:10004400-10018200	Weak transcription	NHLF	lung
34	chr1:10004400-10021200	Weak transcription	HSMM	muscle
35	chr1:10004400-10031600	Weak transcription	Fetal Intestine Large	intestine
36	chr1:10004600-10007000	Weak transcription	Primary B cells from cord blood	blood
37	chr1:10004600-10007200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr1:10004600-10007400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:10004600-10007400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:10004600-10007400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:10004600-10007400	Weak transcription	Brain Hippocampus Middle	brain
42	chr1:10004600-10009400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:10004600-10009800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:10004600-10010400	Weak transcription	Primary T cells from cord blood	blood
45	chr1:10004600-10010400	Weak transcription	Thymus	Thymus
46	chr1:10004600-10010600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:10004600-10010600	Weak transcription	NHDF-Ad	bronchial
48	chr1:10004600-10010600	Weak transcription	Osteobl	bone
49	chr1:10004600-10021000	Weak transcription	HSMMtube	muscle
50	chr1:10004600-10032400	Weak transcription	Placenta Amnion	Placenta Amnion

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