Variant report

Variant	rs2605141
Chromosome Location	chr17:18164239-18164240
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	BCLAF1	chr17:18164213-18164637	GM12878	blood:	n/a	n/a
2	CEBPB	chr17:18164203-18164403	H1-hESC	embryonic stem cell:	n/a	n/a
3	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
4	CHD2	chr17:18163478-18164456	GM12878	blood:	n/a	n/a
5	MAX	chr17:18162938-18164957	Hela-S3	cervix:	n/a	chr17:18164010-18164020
6	POLR2A	chr17:18164154-18164432	GM12891	blood:	n/a	n/a
7	TAF1	chr17:18163479-18164572	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr17:18163324-18164436	K562	blood:	n/a	chr17:18164010-18164020
9	HCFC1	chr17:18163548-18164683	K562	blood:	n/a	n/a
10	POLR2A	chr17:18163516-18164431	HepG2	liver:	n/a	n/a
11	POLR2A	chr17:18163812-18164500	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr17:18163576-18164633	HepG2	liver:	n/a	chr17:18164010-18164020
13	PBX3	chr17:18163476-18164313	A549	lung:	n/a	chr17:18163828-18163837
14	SIN3AK20	chr17:18163411-18165049	MCF-7	breast:	n/a	n/a
15	BRCA1	chr17:18163000-18164781	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr17:18163519-18164617	GM12878	blood:	n/a	n/a
17	MAX	chr17:18163025-18164761	NB4	blood:	n/a	chr17:18164010-18164020
18	SIN3AK20	chr17:18163453-18164671	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZMIZ1	chr17:18163580-18164305	K562	blood:	n/a	n/a
20	RCOR1	chr17:18162901-18164918	Hela-S3	cervix:	n/a	n/a
21	TEAD4	chr17:18162897-18164348	ECC-1	luminal epithelium:	n/a	n/a
22	TCF12	chr17:18162902-18165013	ECC-1	luminal epithelium:	n/a	n/a
23	RCOR1	chr17:18163486-18164250	K562	blood:	n/a	n/a
24	UBTF	chr17:18163571-18164737	K562	blood:	n/a	n/a
25	BACH1	chr17:18163997-18164825	H1-hESC	embryonic stem cell:	n/a	n/a
26	EGR1	chr17:18163834-18164408	GM12878	blood:	n/a	chr17:18164206-18164219
27	POLR2A	chr17:18163829-18164564	GM12891	blood:	n/a	n/a
28	MAX	chr17:18162896-18165104	A549	lung:	n/a	chr17:18164010-18164020
29	MAX	chr17:18162954-18164982	ECC-1	luminal epithelium:	n/a	chr17:18164010-18164020
30	TCF12	chr17:18163406-18164768	A549	lung:	n/a	n/a
31	RFX5	chr17:18163565-18164495	GM12878	blood:	n/a	n/a
32	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
33	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
34	BRCA1	chr17:18163654-18164537	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr17:18163839-18164464	GM12878	blood:	n/a	n/a
36	POLR2A	chr17:18163585-18164358	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr17:18162881-18164958	Hela-S3	cervix:	n/a	n/a
38	MAX	chr17:18162901-18165049	ECC-1	luminal epithelium:	n/a	chr17:18164010-18164020
39	POLR2A	chr17:18163488-18164880	ECC-1	luminal epithelium:	n/a	n/a
40	IRF1	chr17:18163481-18164300	K562	blood:	n/a	chr17:18163829-18163838 chr17:18163810-18163824 chr17:18164125-18164139
41	POU2F2	chr17:18164066-18164505	GM12878	blood:	n/a	n/a
42	SIN3AK20	chr17:18163792-18164288	A549	lung:	n/a	n/a
43	TCF3	chr17:18163510-18164415	GM12878	blood:	n/a	chr17:18163851-18163867
44	GTF2F1	chr17:18163556-18164342	H1-hESC	embryonic stem cell:	n/a	n/a
45	RFX5	chr17:18162977-18164906	Hela-S3	cervix:	n/a	chr17:18164719-18164733 chr17:18164718-18164734 chr17:18164723-18164732
46	TBP	chr17:18163450-18164765	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr17:18163618-18164414	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr17:18163580-18164491	GM12878	blood:	n/a	n/a
49	MAX	chr17:18162989-18164476	HepG2	liver:	n/a	chr17:18164010-18164020
50	MAX	chr17:18163599-18164309	K562	blood:	n/a	chr17:18164010-18164020

No.	Distal block	Cell Line	Cell type
1	chr17:18085197..18089449-chr17:18160313..18164902,6	K562	blood:
2	chr17:18127100..18135567-chr17:18158023..18168767,25	MCF-7	breast:
3	chr17:18156705..18166530-chr17:18215131..18220177,19	MCF-7	breast:
4	chr17:18085249..18088032-chr17:18163903..18166046,2	MCF-7	breast:
5	chr17:18161909..18165526-chr17:18209408..18212171,3	MCF-7	breast:
6	chr17:18126073..18132705-chr17:18158327..18165323,14	MCF-7	breast:
7	chr17:18162871..18165268-chr17:18208056..18210567,2	MCF-7	breast:
8	chr17:18164143..18168210-chr17:18170342..18172063,4	K562	blood:
9	chr17:18158589..18161919-chr17:18164225..18167330,4	K562	blood:
10	chr17:18127671..18130325-chr17:18161981..18165246,3	K562	blood:
11	chr13:60970043..60970937-chr17:18164008..18164555,2	HCT-116	colon:
12	chr17:18159194..18166260-chr17:18215929..18222740,16	MCF-7	breast:

Variant related genes	Relation type
MIEF2	TF binding region
FLII	TF binding region
ENSG00000131899	Chromatin interaction
ENSG00000266677	Chromatin interaction
ENSG00000083544	Chromatin interaction
ENSG00000177302	Chromatin interaction
ENSG00000177731	Chromatin interaction
ENSG00000091542	Chromatin interaction
ENSG00000237382	Chromatin interaction
ENSG00000228000	Chromatin interaction
ENSG00000260647	Chromatin interaction
ENSG00000176994	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12946752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12950117	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1563632	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1563634	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1682280	0.80[LWK][hapmap];0.85[TSI][hapmap]
rs2071241	0.82[ASW][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2245430	0.93[GIH][hapmap]
rs2273027	0.82[JPT][hapmap]
rs2473656	0.93[GIH][hapmap]
rs2605143	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2605144	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2605145	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3764404	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924846	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4925144	0.87[GIH][hapmap]
rs4925166	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925179	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6502647	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs669340	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs712274	0.86[GIH][hapmap]
rs7212104	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7225932	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8076253	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs854800	0.84[GIH][hapmap]
rs854802	0.84[GIH][hapmap]
rs854803	0.84[GIH][hapmap]
rs921985	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2605141	SHMT1	cis	Esophagus Muscularis	GTEx
rs2605141	SHMT1	cis	lymphoblastoid	seeQTL
rs2605141	FAM106A	cis	Thyroid	GTEx
rs2605141	LOC162632	cis	parietal	SCAN
rs2605141	SHMT1	cis	multi-tissue	Pritchard
rs2605141	SHMT1	cis	Whole Blood	GTEx
rs2605141	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs2605141	SHMT1	cis	parietal	SCAN
rs2605141	USP32P2	cis	Whole Blood	GTEx
rs2605141	TOP3A	cis	cerebellum	SCAN
rs2605141	SHMT1	cis	Muscle Skeletal	GTEx
rs2605141	LOC162632	cis	cerebellum	SCAN
rs2605141	SHMT1	cis	Artery Tibial	GTEx
rs2605141	SHMT1	cis	Nerve Tibial	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	chr17:18161600-18164400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:18163000-18164400	Active TSS	Fetal Brain Female	brain
5	chr17:18163000-18165800	Flanking Active TSS	Dnd41	blood
6	chr17:18163200-18164800	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr17:18163200-18165000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr17:18163400-18164800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:18163400-18164800	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr17:18163400-18164800	Active TSS	Ovary	ovary
11	chr17:18163400-18165000	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr17:18163400-18165000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr17:18163400-18165200	Active TSS	H9 Cell Line	embryonic stem cell
14	chr17:18163600-18164400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr17:18163600-18164400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr17:18163600-18164400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr17:18163600-18164400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr17:18163600-18164600	Active TSS	H1 Cell Line	embryonic stem cell
19	chr17:18163600-18164600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr17:18163600-18164600	Active TSS	Brain Angular Gyrus	brain
21	chr17:18163600-18164600	Active TSS	Right Atrium	heart
22	chr17:18163600-18164600	Bivalent/Poised TSS	HepG2	liver
23	chr17:18163600-18164800	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr17:18163600-18164800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr17:18163600-18164800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr17:18163600-18164800	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr17:18163600-18164800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr17:18163600-18164800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr17:18163600-18164800	Active TSS	Aorta	Aorta
30	chr17:18163600-18164800	Active TSS	Fetal Intestine Small	intestine
31	chr17:18163600-18164800	Active TSS	Fetal Kidney	kidney
32	chr17:18163600-18164800	Active TSS	Psoas Muscle	Psoas
33	chr17:18163600-18164800	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr17:18163600-18164800	Active TSS	Small Intestine	intestine
35	chr17:18163600-18164800	Active TSS	Hela-S3	cervix
36	chr17:18163600-18164800	Active TSS	HSMMtube	muscle
37	chr17:18163600-18165000	Active TSS	Placenta Amnion	Placenta Amnion
38	chr17:18163600-18165200	Active TSS	iPS-20b Cell Line	embryonic stem cell
39	chr17:18163800-18164400	Active TSS	Primary T cells from cord blood	blood
40	chr17:18163800-18164400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr17:18163800-18164400	Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr17:18163800-18164400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr17:18163800-18164400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr17:18163800-18164400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr17:18163800-18164400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr17:18163800-18164400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr17:18163800-18164400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr17:18163800-18164400	Active TSS	Adipose Nuclei	Adipose
49	chr17:18163800-18164400	Active TSS	Brain Cingulate Gyrus	brain
50	chr17:18163800-18164400	Active TSS	Brain Substantia Nigra	brain

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