Variant report

Variant	rs73092953
Chromosome Location	chr1:228280632-228280633
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228274276-228290284	K562	blood:	n/a	n/a
2	POLR2A	chr1:228274933-228281306	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:228279300-228281328	K562	blood:	n/a	n/a
4	POLR2A	chr1:228280013-228280712	GM12892	blood:	n/a	n/a
5	FOXA1	chr1:228280567-228281043	T-47D	breast:	n/a	n/a
6	POLR2A	chr1:228279963-228280678	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:228280021-228280685	GM12891	blood:	n/a	n/a
8	POLR2A	chr1:228274170-228289426	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:228279934-228280751	GM12891	blood:	n/a	n/a
10	CBX3	chr1:228280432-228280863	K562	blood:	n/a	n/a
11	POLR2A	chr1:228279745-228282720	K562	blood:	n/a	n/a
12	POLR2A	chr1:228276366-228280674	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:228279922-228281309	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:228279658-228280645	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:228279806-228282603	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:228280254-228281326	HL-60	blood:	n/a	n/a
17	HEY1	chr1:228280011-228280655	K562	blood:	n/a	n/a
18	POLR2A	chr1:228279814-228281389	GM12892	blood:	n/a	n/a
19	POLR2A	chr1:228279964-228280660	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr1:228275014-228282866	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:228279821-228281368	GM12891	blood:	n/a	n/a
22	POLR2A	chr1:228280081-228281290	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:228280043-228281427	K562	blood:	n/a	n/a
24	POLR2A	chr1:228276361-228281309	A549	lung:	n/a	n/a
25	POLR2A	chr1:228280102-228280681	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr1:228279831-228281377	GM12892	blood:	n/a	n/a
27	POLR2A	chr1:228279792-228281560	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr1:228279778-228280672	K562	blood:	n/a	n/a
29	POLR2A	chr1:228274271-228281353	HepG2	liver:	n/a	n/a
30	POLR2A	chr1:228280528-228281133	IMR90	lung:	n/a	n/a
31	POLR2A	chr1:228279831-228281430	GM12892	blood:	n/a	n/a
32	POLR2A	chr1:228280451-228280658	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr1:228279692-228281364	K562	blood:	n/a	n/a
34	POLR2A	chr1:228280393-228280679	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228279258..228282133-chr1:228294135..228296002,2	MCF-7	breast:
2	chr1:228280178..228282214-chr1:228355468..228357999,2	K562	blood:
3	chr1:228279049..228280694-chr1:228350919..228353208,2	MCF-7	breast:
4	chr1:228279450..228280981-chr1:228352924..228354648,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR3620	TF binding region
ENSG00000162910	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000181873	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2231715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2231720	1.00[AMR][1000 genomes]
rs56756911	1.00[AMR][1000 genomes]
rs56832724	1.00[AMR][1000 genomes]
rs56986798	1.00[AMR][1000 genomes]
rs57053910	1.00[AMR][1000 genomes]
rs57114383	1.00[AFR][1000 genomes]
rs59699324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61413658	1.00[AMR][1000 genomes]
rs6694537	1.00[AMR][1000 genomes]
rs6704401	1.00[AMR][1000 genomes]
rs73092912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092923	1.00[AMR][1000 genomes]
rs73092944	1.00[AMR][1000 genomes]
rs73092954	1.00[AMR][1000 genomes]
rs73092957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092959	1.00[AMR][1000 genomes]
rs73092999	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73095404	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73095424	1.00[AMR][1000 genomes]
rs73095429	1.00[AMR][1000 genomes]
rs73095437	1.00[AMR][1000 genomes]
rs73095449	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	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised 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
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228272400-228284400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:228273000-228284200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:228273400-228285200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:228273600-228281800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:228274200-228281200	Genic enhancers	Liver	Liver
6	chr1:228275200-228280800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:228275200-228282000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:228275400-228281200	Genic enhancers	Gastric	stomach
9	chr1:228275400-228281400	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr1:228275600-228281200	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr1:228275800-228281000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:228275800-228286600	Weak transcription	Fetal Kidney	kidney
13	chr1:228276000-228281000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:228276000-228281200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr1:228276000-228281400	Genic enhancers	Placenta	Placenta
16	chr1:228276200-228281200	Enhancers	Right Atrium	heart
17	chr1:228276400-228281400	Genic enhancers	Lung	lung
18	chr1:228276600-228281200	Genic enhancers	NHEK	skin
19	chr1:228276600-228281800	Weak transcription	Fetal Lung	lung
20	chr1:228276600-228285000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:228276800-228281200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:228276800-228281800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:228276800-228290200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:228277000-228281200	Enhancers	Stomach Mucosa	stomach
25	chr1:228277200-228290000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:228277600-228289200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:228277800-228281200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr1:228278000-228280800	Genic enhancers	Rectal Mucosa Donor 29	rectum
29	chr1:228278000-228281200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:228278000-228281400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:228278000-228289400	Genic enhancers	Pancreas	Pancrea
32	chr1:228278200-228281000	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr1:228278400-228281400	Genic enhancers	HMEC	breast
34	chr1:228278400-228282200	Weak transcription	Aorta	Aorta
35	chr1:228278600-228281200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:228278600-228281800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:228278800-228282000	Strong transcription	NHDF-Ad	bronchial
38	chr1:228278800-228282800	ZNF genes & repeats	GM12878-XiMat	blood
39	chr1:228278800-228283000	ZNF genes & repeats	Dnd41	blood
40	chr1:228278800-228283600	Weak transcription	Ovary	ovary
41	chr1:228279000-228281000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr1:228279000-228281000	Strong transcription	NHLF	lung
43	chr1:228279000-228282200	Genic enhancers	Spleen	Spleen
44	chr1:228279000-228285000	Weak transcription	HSMMtube	muscle
45	chr1:228279200-228280800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:228279200-228281000	Strong transcription	Fetal Intestine Large	intestine
47	chr1:228279200-228281000	Strong transcription	Fetal Intestine Small	intestine
48	chr1:228279200-228281000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr1:228279200-228287800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:228279400-228281200	Genic enhancers	Duodenum Mucosa	Duodenum

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