Variant report

Variant	rs2605144
Chromosome Location	chr17:18170948-18170949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:18169887-18175074	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr17:18170684-18170976	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr17:18170903-18172779	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr17:18170622-18170973	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr17:18170686-18171034	A549	lung:	n/a	n/a
6	POLR2A	chr17:18170721-18172060	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr17:18170623-18172026	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr17:18170771-18173049	U87	brain:	n/a	n/a
9	POLR2A	chr17:18170846-18171587	U87	brain:	n/a	n/a
10	POLR2A	chr17:18170708-18171116	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr17:18170539-18175104	A549	lung:	n/a	n/a
12	POLR2A	chr17:18170671-18172775	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr17:18170660-18171532	GM12878	blood:	n/a	n/a
14	POLR2A	chr17:18170700-18171328	K562	blood:	n/a	n/a
15	POLR2A	chr17:18170621-18172034	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr17:18170699-18172629	GM12878	blood:	n/a	n/a
17	POLR2A	chr17:18170711-18171096	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr17:18170720-18170988	GM12878	blood:	n/a	n/a
19	POLR2A	chr17:18170551-18171042	GM12892	blood:	n/a	n/a
20	POLR2A	chr17:18170768-18171719	HepG2	liver:	n/a	n/a
21	POLR2A	chr17:18170337-18171582	HepG2	liver:	n/a	n/a
22	POLR2A	chr17:18170757-18171109	PANC-1	pancreas:	n/a	n/a
23	CTCF	chr17:18170860-18171010	HEK293	kidney:	n/a	n/a
24	POLR2A	chr17:18170792-18173155	U87	brain:	n/a	n/a
25	POLR2A	chr17:18170779-18171808	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr17:18170736-18171069	HL-60	blood:	n/a	n/a
27	POLR2A	chr17:18170640-18172074	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr17:18170863-18171587	U87	brain:	n/a	n/a
29	POLR2A	chr17:18170675-18171897	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr17:18170716-18174376	MCF-7	breast:	n/a	n/a
31	POLR2A	chr17:18170683-18171675	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr17:18170739-18171031	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr17:18170801-18171091	HCT-116	colon:	n/a	n/a
34	POLR2A	chr17:18169948-18175094	K562	blood:	n/a	n/a
35	CTCF	chr17:18170891-18170962	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr17:18170302-18171873	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:18164143..18168210-chr17:18170342..18172063,4	K562	blood:
2	chr17:18127264..18129965-chr17:18170745..18172525,2	K562	blood:
3	chr17:18159414..18161817-chr17:18169101..18171467,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260647	TF binding region
ENSG00000177427	Chromatin interaction
ENSG00000177731	Chromatin interaction
ENSG00000131899	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12946752	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12950117	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1563632	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];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1563634	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071241	0.86[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.81[MKK][hapmap];0.87[ASN][1000 genomes]
rs2245430	0.93[GIH][hapmap]
rs2273027	0.87[JPT][hapmap]
rs2473656	0.93[GIH][hapmap]
rs2605141	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]
rs2605143	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605145	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764404	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924846	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4925144	0.87[GIH][hapmap]
rs4925166	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925179	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6502647	0.88[EUR][1000 genomes]
rs6502650	0.81[AMR][1000 genomes]
rs669340	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs712274	0.87[GIH][hapmap]
rs7212104	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7225932	0.82[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8065874	0.82[JPT][hapmap]
rs8076253	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs854800	0.85[GIH][hapmap]
rs854802	0.85[GIH][hapmap]
rs854803	0.85[GIH][hapmap]
rs921985	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
10	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
11	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2605144	FAM106A	cis	Thyroid	GTEx
rs2605144	SHMT1	cis	Whole Blood	GTEx
rs2605144	SHMT1	cis	Artery Tibial	GTEx
rs2605144	SHMT1	cis	Esophagus Muscularis	GTEx
rs2605144	SHMT1	cis	multi-tissue	Pritchard
rs2605144	USP32P2	cis	Whole Blood	GTEx
rs2605144	SHMT1	cis	lymphoblastoid	seeQTL
rs2605144	LGALS9C	cis	Whole Blood	GTEx
rs2605144	SHMT1	cis	Muscle Skeletal	GTEx
rs2605144	SHMT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18165000-18176600	Weak transcription	HUVEC	blood vessel
2	chr17:18165200-18175400	Weak transcription	Fetal Kidney	kidney
3	chr17:18165200-18176400	Weak transcription	K562	blood
4	chr17:18165400-18171400	Weak transcription	NH-A	brain
5	chr17:18165400-18177600	Weak transcription	Small Intestine	intestine
6	chr17:18165600-18181400	Weak transcription	Psoas Muscle	Psoas
7	chr17:18165800-18171400	Strong transcription	Fetal Stomach	stomach
8	chr17:18165800-18173400	Weak transcription	HSMM	muscle
9	chr17:18165800-18175800	Weak transcription	GM12878-XiMat	blood
10	chr17:18165800-18182800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr17:18166000-18173600	Weak transcription	Hela-S3	cervix
12	chr17:18166000-18179600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr17:18166000-18183800	Weak transcription	Fetal Brain Male	brain
14	chr17:18166200-18171400	Strong transcription	Brain Germinal Matrix	brain
15	chr17:18166200-18183600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr17:18166400-18182600	Strong transcription	Fetal Brain Female	brain
17	chr17:18166600-18171000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
18	chr17:18167000-18188200	Weak transcription	Stomach Mucosa	stomach
19	chr17:18167200-18171000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr17:18168600-18171000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr17:18168600-18171400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr17:18168600-18171400	Weak transcription	HMEC	breast
23	chr17:18168600-18173400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr17:18168800-18171000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr17:18168800-18171200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr17:18168800-18171400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr17:18168800-18171400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr17:18168800-18171400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr17:18168800-18171600	Weak transcription	Osteobl	bone
30	chr17:18168800-18173400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr17:18168800-18173600	Weak transcription	A549	lung
32	chr17:18168800-18174000	Weak transcription	Dnd41	blood
33	chr17:18168800-18176400	Weak transcription	Primary B cells from cord blood	blood
34	chr17:18168800-18177600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr17:18168800-18179200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr17:18168800-18179400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr17:18168800-18183200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr17:18169000-18171200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr17:18169000-18171200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr17:18169000-18171200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr17:18169000-18173400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr17:18169000-18173400	Weak transcription	Brain Anterior Caudate	brain
43	chr17:18169000-18173400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr17:18169000-18173600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr17:18169000-18174800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr17:18169000-18174800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr17:18169000-18175800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr17:18169000-18176200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr17:18169000-18176200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr17:18169000-18176200	Weak transcription	Brain Substantia Nigra	brain

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