Variant report

Variant	rs17236473
Chromosome Location	chr3:160165608-160165609
allele	G/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	GATA1	chr3:160165244-160165860	PBDE	blood:	n/a	chr3:160165621-160165638 chr3:160165558-160165565
2	MAZ	chr3:160165418-160165612	K562	blood:	n/a	n/a
3	JUND	chr3:160165431-160165710	K562	blood:	n/a	chr3:160165555-160165563 chr3:160165554-160165564 chr3:160165554-160165564 chr3:160165553-160165565
4	FOS	chr3:160165386-160165717	MCF10A-Er-Src	breast:	n/a	chr3:160165555-160165563 chr3:160165554-160165564 chr3:160165554-160165564 chr3:160165553-160165565
5	TAL1	chr3:160165438-160165807	K562	blood:	n/a	chr3:160165621-160165639
6	CEBPB	chr3:160165292-160165647	K562	blood:	n/a	chr3:160165332-160165349 chr3:160165482-160165495
7	JUN	chr3:160165069-160165691	K562	blood:	n/a	chr3:160165555-160165563 chr3:160165554-160165564 chr3:160165554-160165564 chr3:160165553-160165565
8	FOS	chr3:160165444-160165696	MCF10A-Er-Src	breast:	n/a	chr3:160165555-160165563 chr3:160165554-160165564 chr3:160165554-160165564 chr3:160165553-160165565
9	IRF1	chr3:160165283-160165945	K562	blood:	n/a	n/a
10	STAT3	chr3:160165297-160165721	MCF10A-Er-Src	breast:	n/a	chr3:160165436-160165444
11	MAFK	chr3:160165449-160165905	IMR90	lung:	n/a	n/a
12	FOS	chr3:160165311-160165774	MCF10A-Er-Src	breast:	n/a	chr3:160165555-160165563 chr3:160165554-160165564 chr3:160165554-160165564 chr3:160165553-160165565
13	STAT3	chr3:160165278-160165705	MCF10A-Er-Src	breast:	n/a	chr3:160165436-160165444
14	BACH1	chr3:160165346-160165608	K562	blood:	n/a	n/a
15	ARID3A	chr3:160165337-160165880	K562	blood:	n/a	n/a
16	IRF1	chr3:160165388-160165980	K562	blood:	n/a	n/a
17	POLR2A	chr3:160165418-160165618	K562	blood:	n/a	n/a
18	MYC	chr3:160165572-160165956	MCF10A-Er-Src	breast:	n/a	n/a
19	STAT3	chr3:160165304-160165612	MCF10A-Er-Src	breast:	n/a	chr3:160165436-160165444
20	FOS	chr3:160165300-160165729	MCF10A-Er-Src	breast:	n/a	chr3:160165555-160165563 chr3:160165554-160165564 chr3:160165554-160165564 chr3:160165553-160165565
21	MAFF	chr3:160165340-160165911	K562	blood:	n/a	n/a
22	CEBPB	chr3:160165262-160165665	IMR90	lung:	n/a	chr3:160165332-160165349 chr3:160165482-160165495
23	CUX1	chr3:160165393-160165753	K562	blood:	n/a	n/a
24	MAFK	chr3:160165416-160166242	K562	blood:	n/a	n/a
25	UBTF	chr3:160165598-160165644	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:160121669..160124122-chr3:160164375..160167615,4	MCF-7	breast:
2	chr3:160164299..160166121-chr3:160258126..160260628,2	MCF-7	breast:
3	chr3:160164655..160166493-chr3:160166882..160169855,2	MCF-7	breast:
4	chr3:160116116..160127665-chr3:160158037..160169627,42	K562	blood:
5	chr3:160131935..160134663-chr3:160164828..160167325,4	K562	blood:
6	chr3:160129823..160131847-chr3:160164070..160166164,2	K562	blood:
7	chr3:160164471..160170330-chr3:160281681..160284179,8	K562	blood:
8	chr3:160164188..160165743-chr3:160181763..160184603,2	K562	blood:
9	chr3:160116116..160124648-chr3:160162504..160168767,20	K562	blood:

Variant related genes	Relation type
ENSG00000244009	TF binding region
ENSG00000186432	Chromatin interaction
ENSG00000198987	Chromatin interaction
ENSG00000229320	Chromatin interaction
ENSG00000207779	Chromatin interaction
ENSG00000113810	Chromatin interaction
ENSG00000213186	Chromatin interaction
ENSG00000068885	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1047210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10513551	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs11706810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11718121	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12632030	0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13403	0.85[CEU][hapmap]
rs1369666	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1451760	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1451761	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs1451762	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs1551190	0.82[JPT][hapmap]
rs17236544	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs17570467	0.81[CEU][hapmap]
rs17826221	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1882126	0.81[CEU][hapmap]
rs1882127	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs1920642	0.84[JPT][hapmap]
rs1920664	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs1953506	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs1971128	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2152425	0.83[JPT][hapmap]
rs2279457	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs2305407	0.88[CEU][hapmap];0.89[JPT][hapmap]
rs3732706	0.92[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3773372	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs3851365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3851366	0.85[CEU][hapmap]
rs4679654	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4679881	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs4679885	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs4679890	0.80[CEU][hapmap]
rs4679891	0.81[JPT][hapmap]
rs4679899	0.82[CEU][hapmap];0.85[JPT][hapmap]
rs4680576	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs4680579	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs4680580	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs4680585	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs4680588	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs4680589	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4680591	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55992947	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56156703	0.85[EUR][1000 genomes]
rs56394279	0.83[AMR][1000 genomes]
rs6441313	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs6441314	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs6441319	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs6441320	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs6441324	0.84[JPT][hapmap]
rs6768975	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs6785881	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6790951	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6791056	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6791261	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs6793560	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs6798183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6798668	0.81[CEU][hapmap]
rs6801300	0.82[JPT][hapmap]
rs6803828	0.86[CEU][hapmap];0.84[JPT][hapmap]
rs6809153	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs721023	0.84[JPT][hapmap]
rs7355951	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7611130	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs7618974	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs7620828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7621724	0.85[JPT][hapmap]
rs7624902	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs7627555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7627756	0.81[CEU][hapmap]
rs7629	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs7631792	0.85[CEU][hapmap]
rs7634108	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs7634826	0.85[CEU][hapmap]
rs7643779	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs7647873	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs869467	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs869468	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs9862595	0.84[JPT][hapmap]
rs9968151	0.85[CEU][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17236473	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160130000-160166200	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:160140800-160166600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:160143600-160166600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:160145600-160166800	Weak transcription	Right Atrium	heart
5	chr3:160146000-160167000	Weak transcription	Pancreas	Pancrea
6	chr3:160146400-160166200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:160147000-160166200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:160150600-160166000	Weak transcription	Fetal Brain Female	brain
9	chr3:160151000-160166600	Weak transcription	Small Intestine	intestine
10	chr3:160151000-160166800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:160152400-160166000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:160152600-160166200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:160153200-160166200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:160153400-160166600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:160154600-160166400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:160155000-160166600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:160155000-160167000	Weak transcription	Placenta	Placenta
18	chr3:160156800-160166200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:160157000-160166600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:160157000-160166600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:160158800-160166400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr3:160161000-160166400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:160161000-160166600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:160162600-160166000	Weak transcription	HepG2	liver
25	chr3:160162600-160166200	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:160162600-160166800	Weak transcription	Ovary	ovary
27	chr3:160163000-160166200	Weak transcription	Fetal Intestine Large	intestine
28	chr3:160163200-160166600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:160163800-160166000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr3:160163800-160166000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr3:160163800-160166200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:160163800-160166200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:160163800-160166800	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr3:160164000-160166000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr3:160164200-160166200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr3:160164200-160166800	Enhancers	Fetal Heart	heart
37	chr3:160164400-160166200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
38	chr3:160164400-160166200	Enhancers	Fetal Lung	lung
39	chr3:160164600-160166400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
40	chr3:160164600-160166600	Active TSS	Brain Hippocampus Middle	brain
41	chr3:160164600-160166800	Active TSS	Brain Substantia Nigra	brain
42	chr3:160164600-160167800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:160164600-160168200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:160164800-160166000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:160164800-160166000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr3:160164800-160166000	Weak transcription	Fetal Stomach	stomach
47	chr3:160164800-160166000	Weak transcription	Thymus	Thymus
48	chr3:160164800-160166200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr3:160164800-160166200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:160164800-160166200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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