Variant report

Variant	rs2872361
Chromosome Location	chr1:228293722-228293723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228290521-228294679	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr1:228293593-228293909	H1-hESC	embryonic stem cell:	n/a	n/a
3	HEY1	chr1:228293631-228293859	K562	blood:	n/a	n/a
4	POLR2A	chr1:228293658-228294087	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:228292437-228293997	GM12891	blood:	n/a	n/a
6	POLR2A	chr1:228293618-228293843	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:228284138-228294734	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:228290729-228294672	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:228293534-228294278	HL-60	blood:	n/a	n/a
10	POLR2A	chr1:228292241-228293966	K562	blood:	n/a	n/a
11	POLR2A	chr1:228291694-228293754	GM12891	blood:	n/a	n/a
12	POLR2A	chr1:228291713-228293928	K562	blood:	n/a	n/a
13	POLR2A	chr1:228283726-228293977	K562	blood:	n/a	n/a
14	POLR2A	chr1:228292723-228294376	K562	blood:	n/a	n/a
15	POLR2A	chr1:228291632-228294040	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr1:228293709-228293766	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr1:228292911-228293983	K562	blood:	n/a	n/a
18	POLR2A	chr1:228289866-228293896	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:228291595-228294465	HepG2	liver:	n/a	n/a
20	POLR2A	chr1:228290818-228294408	K562	blood:	n/a	n/a
21	POLR2A	chr1:228293176-228293989	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr1:228291654-228293974	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:228293388-228293970	GM12892	blood:	n/a	n/a
24	POLR2A	chr1:228291406-228294664	K562	blood:	n/a	n/a
25	POLR2A	chr1:228292569-228293822	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:228292365-228294372	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:228290240..228294197-chr1:228325970..228329742,3	MCF-7	breast:
2	chr1:228292983..228294840-chr1:228295520..228297774,2	MCF-7	breast:
3	chr1:228293306..228296150-chr1:228462712..228464969,2	K562	blood:
4	chr1:228288384..228298705-chr1:228351640..228357240,26	K562	blood:

No data

Variant related genes	Relation type
C1orf35	TF binding region
ENSG00000203684	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000269934	Chromatin interaction
ENSG00000154358	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000143774	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1342350	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4394650	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs61743220	1.00[AFR][1000 genomes]
rs697763	1.00[YRI][hapmap]
rs708109	1.00[YRI][hapmap]

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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228291400-228296400	Weak transcription	Aorta	Aorta
2	chr1:228291600-228296000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:228291800-228293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:228291800-228293800	Weak transcription	HSMMtube	muscle
5	chr1:228291800-228294000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:228291800-228294000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:228291800-228294000	Weak transcription	HMEC	breast
8	chr1:228291800-228295600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:228291800-228295600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:228291800-228296200	Weak transcription	NH-A	brain
11	chr1:228291800-228296400	Weak transcription	Small Intestine	intestine
12	chr1:228292000-228293800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:228292000-228293800	Weak transcription	Brain Angular Gyrus	brain
14	chr1:228292000-228294200	Weak transcription	HSMM	muscle
15	chr1:228292000-228295400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:228292000-228295800	Weak transcription	Fetal Brain Male	brain
17	chr1:228292000-228296000	Weak transcription	Fetal Kidney	kidney
18	chr1:228292000-228296000	Weak transcription	HUVEC	blood vessel
19	chr1:228292000-228296200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:228292000-228296200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:228292200-228293800	Weak transcription	Primary B cells from cord blood	blood
22	chr1:228292200-228293800	Weak transcription	Colonic Mucosa	Colon
23	chr1:228292200-228294200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:228292200-228295400	Weak transcription	Hela-S3	cervix
25	chr1:228292200-228295600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:228292200-228295600	Weak transcription	NHEK	skin
27	chr1:228292200-228295800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:228292200-228295800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:228292200-228296000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:228292200-228296200	Weak transcription	Psoas Muscle	Psoas
31	chr1:228292400-228293800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:228292400-228294000	Weak transcription	HepG2	liver
33	chr1:228292400-228295600	Strong transcription	Fetal Stomach	stomach
34	chr1:228292400-228295800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:228292600-228294200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:228292600-228294600	Strong transcription	A549	lung
37	chr1:228292600-228295400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:228292600-228295600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:228292600-228295600	Strong transcription	Fetal Intestine Small	intestine
40	chr1:228292600-228295800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:228292600-228296200	Weak transcription	Right Atrium	heart
42	chr1:228292800-228293800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr1:228292800-228293800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:228292800-228293800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr1:228292800-228294000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:228292800-228294000	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:228292800-228294800	Strong transcription	GM12878-XiMat	blood
48	chr1:228292800-228295400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:228292800-228295400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:228292800-228295400	Strong transcription	Fetal Brain Female	brain

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