Variant report

Variant	rs2290503
Chromosome Location	chr17:18135753-18135754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18135343..18136871-chr17:18137313..18139125,2	MCF-7	breast:
2	chr17:18128887..18137475-chr17:18144772..18151698,11	K562	blood:
3	chr17:18132797..18135774-chr17:18137041..18139017,2	K562	blood:

Variant related genes	Relation type
ENSG00000177731	Chromatin interaction
ENSG00000131899	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11078411	0.90[GIH][hapmap]
rs11078412	0.90[GIH][hapmap]
rs11655588	0.90[GIH][hapmap]
rs11658477	0.96[GIH][hapmap];0.84[TSI][hapmap]
rs11867855	0.81[AMR][1000 genomes]
rs11867895	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11868708	0.94[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11869582	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs11869952	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11872031	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12449313	0.94[CEU][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12451555	0.83[EUR][1000 genomes]
rs12451698	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12600694	0.87[GIH][hapmap]
rs12939851	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13284	0.90[GIH][hapmap]
rs1563371	0.90[GIH][hapmap]
rs16960980	0.90[GIH][hapmap]
rs16960983	0.90[GIH][hapmap]
rs16960986	0.90[GIH][hapmap]
rs16960990	0.90[GIH][hapmap]
rs16961114	0.93[CEU][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16961133	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16961153	0.94[CEU][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1925	0.94[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1962949	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1962950	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2015336	0.90[GIH][hapmap]
rs2071242	0.94[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2273029	0.94[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2290502	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290504	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290505	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2294913	0.94[CEU][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28364628	0.89[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3088233	0.90[GIH][hapmap]
rs35738574	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3817992	0.94[CEU][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3829956	0.94[CEU][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3862147	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3889544	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4386179	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4450455	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4500798	0.89[CEU][hapmap];0.92[JPT][hapmap]
rs4556848	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925151	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925177	0.95[CEU][hapmap];0.94[JPT][hapmap]
rs57490980	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57697650	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59366579	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62072507	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62072509	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62072511	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62072515	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62072537	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62072540	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62072541	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6502640	0.90[GIH][hapmap]
rs6502641	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7211573	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7215678	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7405677	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7498	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8065026	0.96[GIH][hapmap]
rs8077577	0.90[GIH][hapmap]
rs8081042	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8081155	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8081343	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9909104	0.95[CEU][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs9910090	0.95[CEU][hapmap];0.93[JPT][hapmap]
rs9913139	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9913266	0.88[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv1062828	chr17:18098110-18136330	Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv543245	chr17:18098110-18136330	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv907777	chr17:18131087-18163262	Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2290503	LOC162632	cis	cerebellum	SCAN
rs2290503	FLII	cis	parietal	SCAN
rs2290503	TRPV2	cis	cerebellum	SCAN
rs2290503	FLII	cis	cerebellum	SCAN
rs2290503	PLD6	cis	cerebellum	SCAN
rs2290503	SHMT1	cis	lymphoblastoid	seeQTL
rs2290503	SHMT1	cis	cerebellum	SCAN
rs2290503	LOC162632	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18129600-18148400	Weak transcription	Small Intestine	intestine
2	chr17:18129800-18137000	Weak transcription	Aorta	Aorta
3	chr17:18130000-18136000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr17:18130000-18137000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr17:18130000-18137000	Weak transcription	Left Ventricle	heart
6	chr17:18130000-18137200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr17:18130000-18145400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr17:18130000-18148200	Weak transcription	Fetal Kidney	kidney
9	chr17:18130000-18148200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr17:18130000-18149200	Weak transcription	Psoas Muscle	Psoas
11	chr17:18130200-18135800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr17:18130200-18135800	Weak transcription	Pancreas	Pancrea
13	chr17:18130200-18136000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr17:18130200-18136000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr17:18130200-18136000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr17:18130200-18136800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr17:18130200-18137000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr17:18130200-18137000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr17:18130200-18137400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr17:18130200-18137400	Weak transcription	Colonic Mucosa	Colon
21	chr17:18130200-18138000	Weak transcription	HUVEC	blood vessel
22	chr17:18130200-18139600	Weak transcription	Primary B cells from cord blood	blood
23	chr17:18130200-18145600	Weak transcription	A549	lung
24	chr17:18130200-18147000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr17:18130200-18147000	Weak transcription	Liver	Liver
26	chr17:18130200-18150800	Weak transcription	Right Atrium	heart
27	chr17:18130400-18136000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr17:18130400-18136000	Weak transcription	NHLF	lung
29	chr17:18130400-18136200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr17:18130400-18136400	Weak transcription	NHEK	skin
31	chr17:18130400-18136800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr17:18130400-18137400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr17:18130400-18138000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr17:18130400-18138400	Weak transcription	HSMMtube	muscle
35	chr17:18130400-18138600	Weak transcription	HSMM	muscle
36	chr17:18130400-18139200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr17:18130400-18142400	Weak transcription	Fetal Heart	heart
38	chr17:18130400-18146200	Weak transcription	NHDF-Ad	bronchial
39	chr17:18130400-18148200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr17:18130600-18135800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr17:18130600-18135800	Weak transcription	Osteobl	bone
42	chr17:18130600-18136400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr17:18130600-18136800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr17:18130600-18136800	Weak transcription	HMEC	breast
45	chr17:18130600-18137000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr17:18130600-18138600	Weak transcription	NH-A	brain
47	chr17:18130600-18148200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr17:18130800-18135800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr17:18130800-18135800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr17:18130800-18136400	Weak transcription	Fetal Thymus	thymus

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