Variant report

Variant	rs72831943
Chromosome Location	chr17:18164644-18164645
allele	A/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	MEF2A	chr17:18163625-18164772	GM12878	blood:	n/a	chr17:18164366-18164381 chr17:18164633-18164654 chr17:18164635-18164650 chr17:18164366-18164381 chr17:18164636-18164647 chr17:18164634-18164650 chr17:18164638-18164647
2	MAX	chr17:18162938-18164957	Hela-S3	cervix:	n/a	chr17:18164010-18164020
3	HCFC1	chr17:18163548-18164683	K562	blood:	n/a	n/a
4	GATA3	chr17:18164407-18164771	T-47D	breast:	n/a	chr17:18164677-18164686
5	SIN3AK20	chr17:18163411-18165049	MCF-7	breast:	n/a	n/a
6	BRCA1	chr17:18163000-18164781	Hela-S3	cervix:	n/a	n/a
7	MAX	chr17:18163025-18164761	NB4	blood:	n/a	chr17:18164010-18164020
8	SIN3AK20	chr17:18163453-18164671	H1-hESC	embryonic stem cell:	n/a	n/a
9	RCOR1	chr17:18162901-18164918	Hela-S3	cervix:	n/a	n/a
10	TCF12	chr17:18162902-18165013	ECC-1	luminal epithelium:	n/a	n/a
11	UBTF	chr17:18163571-18164737	K562	blood:	n/a	n/a
12	BACH1	chr17:18163997-18164825	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr17:18162896-18165104	A549	lung:	n/a	chr17:18164010-18164020
14	MAX	chr17:18162954-18164982	ECC-1	luminal epithelium:	n/a	chr17:18164010-18164020
15	TCF12	chr17:18163406-18164768	A549	lung:	n/a	n/a
16	SP1	chr17:18162847-18165044	HCT-116	colon:	n/a	chr17:18163818-18163839 chr17:18164204-18164218 chr17:18163810-18163822 chr17:18163812-18163821 chr17:18164125-18164137 chr17:18164125-18164137 chr17:18164126-18164136 chr17:18163778-18163787 chr17:18163811-18163820 chr17:18163807-18163821 chr17:18164126-18164136 chr17:18163810-18163822 chr17:18164159-18164168
17	SP1	chr17:18163396-18164893	A549	lung:	n/a	chr17:18163818-18163839 chr17:18164204-18164218 chr17:18163810-18163822 chr17:18163812-18163821 chr17:18164125-18164137 chr17:18164125-18164137 chr17:18164126-18164136 chr17:18163778-18163787 chr17:18163811-18163820 chr17:18163807-18163821 chr17:18164126-18164136 chr17:18163810-18163822 chr17:18164159-18164168
18	POLR2A	chr17:18162881-18164958	Hela-S3	cervix:	n/a	n/a
19	MAX	chr17:18162901-18165049	ECC-1	luminal epithelium:	n/a	chr17:18164010-18164020
20	EBF1	chr17:18164452-18164941	GM12878	blood:	n/a	n/a
21	POLR2A	chr17:18163488-18164880	ECC-1	luminal epithelium:	n/a	n/a
22	FOS	chr17:18164489-18164845	MCF10A-Er-Src	breast:	n/a	chr17:18164676-18164684 chr17:18164674-18164686 chr17:18164674-18164685
23	RFX5	chr17:18164343-18164852	HepG2	liver:	n/a	chr17:18164719-18164733 chr17:18164718-18164734 chr17:18164723-18164732
24	RFX5	chr17:18162977-18164906	Hela-S3	cervix:	n/a	chr17:18164719-18164733 chr17:18164718-18164734 chr17:18164723-18164732
25	TBP	chr17:18163450-18164765	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr17:18164586-18164663	ProgFib	skin:	n/a	n/a
27	GATA3	chr17:18164278-18165005	MCF-7	breast:	n/a	chr17:18164677-18164686 chr17:18164389-18164399
28	POLR2A	chr17:18163688-18164809	GM12892	blood:	n/a	n/a
29	MAX	chr17:18162931-18164952	Hela-S3	cervix:	n/a	chr17:18164010-18164020
30	RUNX3	chr17:18163452-18164745	GM12878	blood:	n/a	n/a
31	JUND	chr17:18164337-18164899	Hela-S3	cervix:	n/a	chr17:18164676-18164684 chr17:18164674-18164686
32	ESR1	chr17:18164536-18164976	ECC-1	luminal epithelium:	n/a	n/a
33	MAFK	chr17:18163087-18164833	Hela-S3	cervix:	n/a	chr17:18164208-18164223
34	TFAP2C	chr17:18163048-18165130	Hela-S3	cervix:	n/a	n/a
35	MYC	chr17:18164512-18164967	MCF10A-Er-Src	breast:	n/a	n/a
36	HCFC1	chr17:18163395-18165215	Hela-S3	cervix:	n/a	n/a
37	CEBPB	chr17:18164558-18165041	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr17:18163566-18164661	A549	lung:	n/a	n/a
39	MAZ	chr17:18163302-18164861	K562	blood:	n/a	chr17:18164010-18164020
40	FOSL2	chr17:18164312-18164925	A549	lung:	n/a	chr17:18164676-18164684 chr17:18164674-18164686
41	FOSL2	chr17:18164430-18164940	MCF-7	breast:	n/a	chr17:18164676-18164684 chr17:18164674-18164686
42	FOSL1	chr17:18164521-18164797	K562	blood:	n/a	chr17:18164676-18164684 chr17:18164674-18164686 chr17:18164674-18164685
43	POLR2A	chr17:18163268-18166534	Hela-S3	cervix:	n/a	n/a
44	HMGN3	chr17:18163369-18164777	K562	blood:	n/a	chr17:18164674-18164683
45	CHD2	chr17:18162965-18164910	Hela-S3	cervix:	n/a	n/a
46	TCF12	chr17:18163464-18164703	ECC-1	luminal epithelium:	n/a	n/a
47	MAZ	chr17:18163098-18165279	Hela-S3	cervix:	n/a	chr17:18164010-18164020
48	TBL1XR1	chr17:18163911-18164798	K562	blood:	n/a	n/a
49	TAF1	chr17:18163569-18164940	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr17:18164555-18164651	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:18085197..18089449-chr17:18160313..18164902,6	K562	blood:
2	chr17:18164305..18167744-chr17:18176383..18179397,3	K562	blood:
3	chr17:18127100..18135567-chr17:18158023..18168767,25	MCF-7	breast:
4	chr17:18156705..18166530-chr17:18215131..18220177,19	MCF-7	breast:
5	chr17:18085249..18088032-chr17:18163903..18166046,2	MCF-7	breast:
6	chr17:18161909..18165526-chr17:18209408..18212171,3	MCF-7	breast:
7	chr17:18126073..18132705-chr17:18158327..18165323,14	MCF-7	breast:
8	chr17:18162871..18165268-chr17:18208056..18210567,2	MCF-7	breast:
9	chr17:18164143..18168210-chr17:18170342..18172063,4	K562	blood:
10	chr17:18158589..18161919-chr17:18164225..18167330,4	K562	blood:
11	chr17:18127671..18130325-chr17:18161981..18165246,3	K562	blood:
12	chr17:18159194..18166260-chr17:18215929..18222740,16	MCF-7	breast:

Variant related genes	Relation type
FLII	TF binding region
ENSG00000177731	Chromatin interaction
ENSG00000176994	Chromatin interaction
ENSG00000091542	Chromatin interaction
ENSG00000237382	Chromatin interaction
ENSG00000177302	Chromatin interaction
ENSG00000266677	Chromatin interaction
ENSG00000228000	Chromatin interaction
ENSG00000260647	Chromatin interaction
ENSG00000131899	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11555081	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12601400	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12601687	0.84[ASN][1000 genomes]
rs12603682	0.81[ASN][1000 genomes]
rs12603700	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17732686	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17805907	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17806489	0.83[ASN][1000 genomes]
rs2273026	0.83[ASN][1000 genomes]
rs2290507	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2294914	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3088175	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3794773	0.86[ASN][1000 genomes]
rs3889402	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4925157	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs55793748	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs55912774	0.81[ASN][1000 genomes]
rs55940735	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs56074845	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56159325	0.81[ASN][1000 genomes]
rs56230317	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs56355515	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56360702	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs57476545	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs57808902	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58042962	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs60435159	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs67826234	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68165736	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7216214	0.84[ASN][1000 genomes]
rs7217566	0.83[ASN][1000 genomes]
rs73289931	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73289935	0.87[AMR][1000 genomes]
rs73289939	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73289960	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv907775	chr17:18108496-18206234	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv543246	chr17:18121007-18165604	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
10	nsv9503	chr17:18121474-18169166	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
11	nsv907776	chr17:18122485-18170948	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
12	nsv1066718	chr17:18125122-18180807	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs72831943	SHMT1	cis	Whole Blood	GTEx
rs72831943	SMCR7	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18160800-18165000	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr17:18160800-18165200	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr17:18163000-18165800	Flanking Active TSS	Dnd41	blood
4	chr17:18163200-18164800	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr17:18163200-18165000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr17:18163400-18164800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr17:18163400-18164800	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr17:18163400-18164800	Active TSS	Ovary	ovary
9	chr17:18163400-18165000	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr17:18163400-18165000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr17:18163400-18165200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr17:18163600-18164800	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr17:18163600-18164800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr17:18163600-18164800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr17:18163600-18164800	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr17:18163600-18164800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr17:18163600-18164800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr17:18163600-18164800	Active TSS	Aorta	Aorta
19	chr17:18163600-18164800	Active TSS	Fetal Intestine Small	intestine
20	chr17:18163600-18164800	Active TSS	Fetal Kidney	kidney
21	chr17:18163600-18164800	Active TSS	Psoas Muscle	Psoas
22	chr17:18163600-18164800	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr17:18163600-18164800	Active TSS	Small Intestine	intestine
24	chr17:18163600-18164800	Active TSS	Hela-S3	cervix
25	chr17:18163600-18164800	Active TSS	HSMMtube	muscle
26	chr17:18163600-18165000	Active TSS	Placenta Amnion	Placenta Amnion
27	chr17:18163600-18165200	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr17:18163800-18164800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr17:18163800-18164800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr17:18163800-18164800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr17:18163800-18164800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr17:18163800-18164800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr17:18163800-18164800	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr17:18163800-18164800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr17:18163800-18164800	Active TSS	Fetal Intestine Large	intestine
36	chr17:18163800-18164800	Active TSS	Gastric	stomach
37	chr17:18163800-18164800	Active TSS	Lung	lung
38	chr17:18163800-18164800	Active TSS	Right Ventricle	heart
39	chr17:18163800-18164800	Active TSS	Stomach Mucosa	stomach
40	chr17:18163800-18164800	Active TSS	A549	lung
41	chr17:18163800-18164800	Active TSS	GM12878-XiMat	blood
42	chr17:18163800-18164800	Active TSS	HMEC	breast
43	chr17:18163800-18164800	Active TSS	HSMM	muscle
44	chr17:18163800-18164800	Active TSS	K562	blood
45	chr17:18163800-18164800	Active TSS	NHDF-Ad	bronchial
46	chr17:18163800-18164800	Active TSS	NHEK	skin
47	chr17:18163800-18164800	Active TSS	NHLF	lung
48	chr17:18164000-18165000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr17:18164000-18166600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
50	chr17:18164200-18164800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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