Variant report

Variant	rs3123543
Chromosome Location	chr1:212790686-212790687
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:212789915-212790809	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:212789886-212791122	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:212789897-212791142	K562	blood:	n/a	n/a
4	POLR2A	chr1:212790102-212791129	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:212790396-212791003	K562	blood:	n/a	n/a
6	POLR2A	chr1:212790459-212790953	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:212789887-212791090	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:212789963-212791101	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:212789876-212790961	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:212789990-212791089	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:212790032-212790941	K562	blood:	n/a	n/a
12	POLR2A	chr1:212780144-212798001	IMR90	lung:	n/a	n/a
13	POLR2A	chr1:212790668-212790847	K562	blood:	n/a	n/a
14	POLR2A	chr1:212789969-212790733	HCT-116	colon:	n/a	n/a
15	POLR2A	chr1:212787968-212791124	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:212790205-212791025	GM12892	blood:	n/a	n/a
17	POLR2A	chr1:212789869-212796544	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:212782514-212798502	A549	lung:	n/a	n/a
19	POLR2A	chr1:212789864-212791004	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212780858..212783878-chr1:212789179..212792370,4	MCF-7	breast:
2	chr1:212729491..212744666-chr1:212778733..212791648,68	K562	blood:
3	chr1:212694583..212696662-chr1:212790397..212791972,2	K562	blood:
4	chr1:212729172..212744062-chr1:212776412..212791648,77	K562	blood:
5	chr1:212790623..212792984-chr1:212868720..212871202,2	K562	blood:

No data

Variant related genes	Relation type
RN7SL512P	TF binding region
ENSG00000162772	Chromatin interaction
ENSG00000260805	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7533306	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9430097	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS 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	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212783400-212791600	Weak transcription	Ovary	ovary
2	chr1:212783600-212792000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:212784000-212792000	Weak transcription	Esophagus	oesophagus
4	chr1:212784000-212794200	Weak transcription	HUVEC	blood vessel
5	chr1:212784200-212796800	Weak transcription	Stomach Mucosa	stomach
6	chr1:212784800-212794800	Weak transcription	NH-A	brain
7	chr1:212785000-212797000	Weak transcription	Right Atrium	heart
8	chr1:212785000-212801000	Weak transcription	Fetal Heart	heart
9	chr1:212785400-212795600	Weak transcription	A549	lung
10	chr1:212785800-212792400	Weak transcription	Small Intestine	intestine
11	chr1:212786400-212794000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:212786600-212795200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:212786800-212791600	Weak transcription	Fetal Lung	lung
14	chr1:212787000-212794000	Strong transcription	Fetal Intestine Small	intestine
15	chr1:212787000-212794400	Strong transcription	Stomach Smooth Muscle	stomach
16	chr1:212787200-212791600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:212787600-212792400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:212787600-212793800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:212787600-212793800	Strong transcription	Right Ventricle	heart
20	chr1:212787600-212793800	Strong transcription	K562	blood
21	chr1:212787600-212794400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:212787600-212794400	Strong transcription	NHLF	lung
23	chr1:212787600-212795000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:212787800-212791600	Weak transcription	NHDF-Ad	bronchial
25	chr1:212788000-212794200	Strong transcription	Fetal Stomach	stomach
26	chr1:212788200-212792400	Strong transcription	Lung	lung
27	chr1:212788200-212793600	Strong transcription	HepG2	liver
28	chr1:212788200-212794200	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:212788200-212794400	Strong transcription	Adipose Nuclei	Adipose
30	chr1:212788200-212794400	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:212788200-212794600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:212788200-212794600	Strong transcription	Fetal Muscle Leg	muscle
33	chr1:212788200-212794800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:212788200-212795000	Strong transcription	Liver	Liver
35	chr1:212788200-212795200	Strong transcription	Placenta	Placenta
36	chr1:212788400-212791600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:212788400-212792000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:212788400-212792200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:212788400-212792600	Strong transcription	Hela-S3	cervix
40	chr1:212788400-212793000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:212788400-212793200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:212788400-212793200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:212788400-212793400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:212788400-212793400	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr1:212788400-212793600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:212788400-212793600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:212788400-212793800	Strong transcription	Brain Anterior Caudate	brain
48	chr1:212788400-212793800	Strong transcription	Gastric	stomach
49	chr1:212788400-212793800	Strong transcription	Rectal Smooth Muscle	rectum
50	chr1:212788400-212793800	Strong transcription	Sigmoid Colon	Sigmoid Colon

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