Variant report

Variant	rs1050923
Chromosome Location	chr1:153517172-153517173
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:153514448-153518753	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:153516977-153518458	A549	lung:	n/a	n/a
3	POLR2A	chr1:153516727-153518754	SK-N-MC	brain:	n/a	n/a
4	REST	chr1:153517093-153518753	A549	lung:	n/a	chr1:153518621-153518634 chr1:153518563-153518576
5	YY1	chr1:153517104-153518644	A549	lung:	n/a	n/a
6	MAX	chr1:153517155-153518101	ECC-1	luminal epithelium:	n/a	n/a
7	MAFK	chr1:153517169-153517239	K562	blood:	n/a	n/a
8	POLR2A	chr1:153517166-153518620	Hela-S3	cervix:	n/a	n/a
9	USF2	chr1:153516796-153517245	Hela-S3	cervix:	n/a	n/a
10	GTF2F1	chr1:153517047-153518664	Hela-S3	cervix:	n/a	n/a
11	KAP1	chr1:153516981-153517869	K562	blood:	n/a	n/a
12	POLR2A	chr1:153516836-153518740	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:153516716-153518656	ProgFib	skin:	n/a	n/a
14	POLR2A	chr1:153514113-153518626	PANC-1	pancreas:	n/a	n/a
15	CHD2	chr1:153516946-153518327	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:153516714-153518750	HL-60	blood:	n/a	n/a
17	POLR2A	chr1:153517042-153518636	Hela-S3	cervix:	n/a	n/a
18	YY1	chr1:153517149-153517972	ECC-1	luminal epithelium:	n/a	n/a
19	MAX	chr1:153516656-153518729	A549	lung:	n/a	chr1:153517092-153517101
20	MAX	chr1:153516828-153518688	A549	lung:	n/a	chr1:153517092-153517101
21	SP1	chr1:153517055-153517948	H1-hESC	embryonic stem cell:	n/a	chr1:153517568-153517579 chr1:153517617-153517626 chr1:153517725-153517734 chr1:153517616-153517628 chr1:153517616-153517628 chr1:153517616-153517627 chr1:153517720-153517733
22	POLR2A	chr1:153517112-153518622	A549	lung:	n/a	n/a
23	SMARCC1	chr1:153517009-153518647	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr1:153516654-153518595	HCT-116	colon:	n/a	n/a
25	TEAD4	chr1:153517168-153518207	ECC-1	luminal epithelium:	n/a	n/a
26	TCF12	chr1:153516679-153519108	A549	lung:	n/a	n/a
27	POLR2A	chr1:153517149-153517318	A549	lung:	n/a	n/a
28	POLR2A	chr1:153516740-153518708	PBDE	blood:	n/a	n/a
29	POLR2A	chr1:153517077-153518472	ECC-1	luminal epithelium:	n/a	n/a
30	CBX3	chr1:153517150-153518086	K562	blood:	n/a	n/a
31	TCF12	chr1:153517149-153518241	ECC-1	luminal epithelium:	n/a	n/a
32	SMARCB1	chr1:153516920-153518608	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr1:153516293-153518722	PANC-1	pancreas:	n/a	n/a
34	MAX	chr1:153517085-153518328	ECC-1	luminal epithelium:	n/a	chr1:153517092-153517101
35	FOSL2	chr1:153517090-153518658	A549	lung:	n/a	chr1:153517654-153517665
36	SP1	chr1:153517162-153518616	A549	lung:	n/a	chr1:153517568-153517579 chr1:153517617-153517626 chr1:153517725-153517734 chr1:153517616-153517628 chr1:153517616-153517628 chr1:153517616-153517627 chr1:153517720-153517733
37	SP1	chr1:153517153-153518684	A549	lung:	n/a	chr1:153517616-153517628 chr1:153517616-153517627 chr1:153517568-153517579 chr1:153517617-153517626 chr1:153517725-153517734 chr1:153517720-153517733 chr1:153517616-153517628
38	POLR2A	chr1:153516743-153518569	HCT-116	colon:	n/a	n/a
39	NFIC	chr1:153517099-153518367	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153514799..153517187-chr1:153642186..153644842,2	MCF-7	breast:
2	chr1:153516187..153518294-chr1:153538747..153540345,2	K562	blood:
3	chr1:153511083..153513930-chr1:153515986..153517623,2	K562	blood:
4	chr1:153515859..153517501-chr1:153605058..153607945,2	K562	blood:
5	chr1:153516334..153517838-chr1:153905134..153907202,2	MCF-7	breast:
6	chr1:153506339..153510656-chr1:153517043..153519160,4	K562	blood:
7	chr1:153515275..153518447-chr1:153598676..153601896,4	MCF-7	breast:
8	chr1:153505949..153508623-chr1:153516119..153518362,2	K562	blood:
9	chr1:153508634..153510673-chr1:153516202..153519160,2	K562	blood:
10	chr1:153515934..153518266-chr1:153581311..153583180,3	MCF-7	breast:
11	chr1:153515310..153522123-chr1:153537390..153541283,13	MCF-7	breast:

Variant related genes	Relation type
S100A5	TF binding region
ENSG00000238279	Chromatin interaction
ENSG00000196420	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000198837	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000196754	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1047325	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs11488669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16835393	0.82[MEX][hapmap]
rs16835437	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs16835455	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1810765	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs28452456	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28548347	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28594230	0.97[EUR][1000 genomes]
rs28689606	0.97[EUR][1000 genomes]
rs28718953	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36022742	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.94[EUR][1000 genomes]
rs41265162	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41265164	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4595398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4845351	0.82[MEX][hapmap]
rs55955983	0.94[EUR][1000 genomes]
rs56043239	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56057245	0.84[EUR][1000 genomes]
rs56089062	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56350425	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56838169	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57024596	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58056804	0.97[EUR][1000 genomes]
rs58072118	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59376279	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60218214	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60287468	0.97[EUR][1000 genomes]
rs60969679	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61265945	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61558997	0.91[EUR][1000 genomes]
rs6427301	0.94[EUR][1000 genomes]
rs6671398	0.88[EUR][1000 genomes]
rs6684970	0.82[MEX][hapmap]
rs6700310	0.91[EUR][1000 genomes]
rs6702891	0.90[GIH][hapmap]
rs6703014	0.90[GIH][hapmap]
rs73026350	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74115473	0.97[EUR][1000 genomes]
rs74115476	0.91[EUR][1000 genomes]
rs743687	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7518306	0.82[MEX][hapmap]
rs7535476	0.84[EUR][1000 genomes]
rs8401	1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[TSI][hapmap];0.88[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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153509200-153517400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:153509400-153527600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:153511400-153517200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:153512200-153517200	Enhancers	Thymus	Thymus
5	chr1:153512400-153522400	Enhancers	Stomach Mucosa	stomach
6	chr1:153514000-153517200	Weak transcription	GM12878-XiMat	blood
7	chr1:153514800-153517200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:153515000-153517400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:153515000-153517400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
10	chr1:153515000-153518000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:153515200-153517200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:153515400-153517200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:153515400-153517200	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
14	chr1:153515400-153517200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:153515400-153517400	Transcr. at gene 5' and 3'	Hela-S3	cervix
16	chr1:153515400-153518000	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
17	chr1:153515400-153518600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:153515400-153518600	Enhancers	Osteobl	bone
19	chr1:153515400-153522800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:153515400-153523000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:153515600-153517400	Transcr. at gene 5' and 3'	A549	lung
22	chr1:153515600-153517400	Flanking Active TSS	HSMMtube	muscle
23	chr1:153515600-153518200	Enhancers	Fetal Kidney	kidney
24	chr1:153515600-153518800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr1:153515600-153520000	Enhancers	HMEC	breast
26	chr1:153515800-153517200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:153515800-153517200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:153515800-153517200	Enhancers	Right Ventricle	heart
29	chr1:153515800-153518000	Enhancers	Fetal Heart	heart
30	chr1:153516000-153517200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:153516000-153517400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
32	chr1:153516200-153517400	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
33	chr1:153516200-153518600	Enhancers	Fetal Lung	lung
34	chr1:153516200-153520600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:153516400-153517200	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
36	chr1:153516400-153517200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:153516400-153517200	Transcr. at gene 5' and 3'	Spleen	Spleen
38	chr1:153516400-153517200	Enhancers	NHEK	skin
39	chr1:153516400-153517400	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
40	chr1:153516400-153517400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
41	chr1:153516400-153518200	Flanking Active TSS	K562	blood
42	chr1:153516400-153518600	Enhancers	Small Intestine	intestine
43	chr1:153516400-153518800	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr1:153516400-153519000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr1:153516600-153517200	Transcr. at gene 5' and 3'	Aorta	Aorta
46	chr1:153516600-153517200	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr1:153516600-153519000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr1:153516800-153517200	Enhancers	H9 Cell Line	embryonic stem cell
49	chr1:153516800-153517200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood
50	chr1:153516800-153517200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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