Variant report

Variant	rs6043388
Chromosome Location	chr20:1612491-1612492
allele	C/T
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	CEBPB	chr20:1612296-1612538	HepG2	liver:	n/a	n/a
2	STAT3	chr20:1612330-1612530	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr20:1612278-1612582	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr20:1612338-1612585	A549	lung:	n/a	n/a
5	MYC	chr20:1612205-1612597	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr20:1612310-1612560	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr20:1612304-1612572	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr20:1612269-1612589	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr20:1612273-1612594	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr20:1612314-1612537	MCF10A-Er-Src	breast:	n/a	n/a
11	RUNX3	chr20:1612478-1613350	GM12878	blood:	n/a	n/a
12	PRDM1	chr20:1612229-1612582	Hela-S3	cervix:	n/a	chr20:1612387-1612402
13	MYC	chr20:1612294-1612581	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr20:1612260-1612535	MCF10A-Er-Src	breast:	n/a	n/a
15	MYC	chr20:1612466-1613187	NB4	blood:	n/a	n/a
16	CEBPB	chr20:1612231-1612611	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
SIRPG	TF binding region
ENSG00000237914	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2023565	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6043406	0.93[EUR][1000 genomes]
rs6043407	0.82[EUR][1000 genomes]
rs6105421	1.00[CHD][hapmap]
rs62186949	0.95[EUR][1000 genomes]
rs7272255	1.00[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats 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	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv2758509	chr20:1476781-1679256	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv2758777	chr20:1476781-1679256	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv428374	chr20:1476781-1679256	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv912596	chr20:1486637-1877150	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1057036	chr20:1493425-1869281	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv912597	chr20:1500506-1877150	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	nsv510779	chr20:1509330-1613962	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv833894	chr20:1519433-1753366	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic 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	18 gene(s)	inside rSNPs	diseases
11	nsv1063015	chr20:1531131-1674430	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv531473	chr20:1532476-1864506	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong 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	28 gene(s)	inside rSNPs	diseases
13	esv3454857	chr20:1545594-1674850	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	esv3454856	chr20:1545691-1674811	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	esv3454858	chr20:1545691-1674811	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	esv1806656	chr20:1553470-1651867	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	esv3454892	chr20:1585279-1617007	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
18	esv3454893	chr20:1585279-1617007	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6043388	OR1C1	trans	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1605200-1631800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr20:1605800-1612800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:1607600-1627600	Weak transcription	Fetal Thymus	thymus
4	chr20:1607600-1632000	Weak transcription	Spleen	Spleen
5	chr20:1608400-1616800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr20:1608800-1613000	Strong transcription	Primary T cells from cord blood	blood
7	chr20:1610800-1614200	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr20:1610800-1614400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr20:1611200-1612600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr20:1611600-1613200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr20:1611600-1614800	Enhancers	HMEC	breast
12	chr20:1611600-1624800	Weak transcription	Thymus	Thymus
13	chr20:1611800-1612800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr20:1611800-1613400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr20:1611800-1613800	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr20:1612000-1612600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr20:1612000-1612800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr20:1612000-1612800	Enhancers	HUVEC	blood vessel
19	chr20:1612000-1613400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr20:1612000-1613600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr20:1612000-1613600	Enhancers	GM12878-XiMat	blood
22	chr20:1612200-1612600	Enhancers	H9 Cell Line	embryonic stem cell
23	chr20:1612200-1612800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr20:1612200-1612800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
25	chr20:1612200-1612800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr20:1612200-1613200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr20:1612200-1613400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr20:1612200-1613400	Enhancers	H1 Cell Line	embryonic stem cell
29	chr20:1612200-1613400	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr20:1612200-1613400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr20:1612200-1613600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr20:1612200-1613800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr20:1612200-1614800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr20:1612200-1615800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr20:1612400-1612600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr20:1612400-1612600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr20:1612400-1612600	Flanking Active TSS	Hela-S3	cervix
38	chr20:1612400-1613200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr20:1612400-1613200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr20:1612400-1614600	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr20:1612400-1614800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr20:1612400-1616000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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