Variant report

Variant	rs9909104
Chromosome Location	chr17:18248021-18248022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11078411	1.00[GIH][hapmap]
rs11078412	1.00[GIH][hapmap]
rs11078415	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11655588	1.00[GIH][hapmap]
rs11867855	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11868708	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11869515	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11869582	0.82[CEU][hapmap]
rs11869952	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11871761	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12449313	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12450760	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12451555	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12451698	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12451807	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12600694	0.97[GIH][hapmap]
rs13284	1.00[GIH][hapmap]
rs1563371	1.00[GIH][hapmap]
rs16960980	1.00[GIH][hapmap]
rs16960983	1.00[GIH][hapmap]
rs16960986	1.00[GIH][hapmap]
rs16960990	1.00[GIH][hapmap]
rs16961114	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16961133	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16961153	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1925	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1962949	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1962950	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2015336	1.00[GIH][hapmap]
rs2071242	0.89[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap]
rs2273027	0.89[YRI][hapmap]
rs2273029	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290502	0.95[CEU][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs2290503	0.95[CEU][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap]
rs2290505	0.94[JPT][hapmap]
rs2294913	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28364628	0.84[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap]
rs3088233	1.00[GIH][hapmap]
rs3817992	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3829956	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4450455	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs4500798	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925178	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57490980	0.82[EUR][1000 genomes]
rs57697650	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58019181	0.82[ASN][1000 genomes]
rs59366579	0.87[EUR][1000 genomes]
rs62072507	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62072509	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62072511	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62072515	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62072537	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62072540	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62072541	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62072544	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62072545	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62072546	0.80[EUR][1000 genomes]
rs6502640	1.00[GIH][hapmap]
rs7215678	0.89[CEU][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap]
rs7498	1.00[CEU][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs8077577	1.00[GIH][hapmap]
rs8080168	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8081042	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8081155	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8081343	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8082494	0.83[CHB][hapmap]
rs9901160	1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs9901707	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9910090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913139	0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs9913266	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1057081	chr17:18171516-18256347	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS 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	15 gene(s)	inside rSNPs	diseases
6	nsv543247	chr17:18171516-18256347	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1062368	chr17:18180747-18259234	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv833387	chr17:18200081-18378155	Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS 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	34 gene(s)	inside rSNPs	diseases
9	esv1806346	chr17:18200081-18446384	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	esv1812661	chr17:18200081-18446384	Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	nsv428333	chr17:18200081-18446384	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' 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	39 gene(s)	inside rSNPs	diseases
12	nsv427992	chr17:18200081-19192047	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
13	esv2758443	chr17:18234525-18446384	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
14	esv2758677	chr17:18234525-18446384	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
15	esv1829832	chr17:18235992-18405148	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9909104	SHMT1	cis	cerebellum	SCAN
rs9909104	SMCR7	cis	lymphoblastoid	seeQTL
rs9909104	LOC162632	cis	parietal	SCAN
rs9909104	FLII	cis	parietal	SCAN
rs9909104	LOC162632	cis	cerebellum	SCAN
rs9909104	FLII	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18219400-18266000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18222400-18266200	Weak transcription	Small Intestine	intestine
3	chr17:18223600-18265400	Strong transcription	Fetal Stomach	stomach
4	chr17:18223800-18253600	Strong transcription	Thymus	Thymus
5	chr17:18224200-18253000	Weak transcription	Fetal Heart	heart
6	chr17:18224400-18249400	Weak transcription	K562	blood
7	chr17:18228200-18265800	Weak transcription	Fetal Brain Male	brain
8	chr17:18228600-18251400	Weak transcription	HSMMtube	muscle
9	chr17:18228600-18266000	Weak transcription	HSMM	muscle
10	chr17:18228800-18249400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr17:18229000-18266000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr17:18230000-18260000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr17:18230200-18260200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr17:18230200-18265600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:18231000-18266000	Weak transcription	Psoas Muscle	Psoas
16	chr17:18231200-18260600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr17:18234600-18249400	Weak transcription	Osteobl	bone
18	chr17:18235400-18256600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr17:18235800-18265400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr17:18236400-18250000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr17:18236600-18250400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr17:18237600-18260200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr17:18239000-18249800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr17:18239000-18250200	Weak transcription	NHDF-Ad	bronchial
25	chr17:18239400-18248200	Weak transcription	Right Ventricle	heart
26	chr17:18239800-18249600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr17:18242200-18260400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr17:18242400-18252200	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr17:18242400-18252400	Strong transcription	HepG2	liver
30	chr17:18242400-18253000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr17:18242400-18253000	Strong transcription	Adipose Nuclei	Adipose
32	chr17:18242400-18253000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr17:18242400-18258200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr17:18242400-18259600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr17:18242400-18264000	Strong transcription	Fetal Thymus	thymus
36	chr17:18242600-18252200	Strong transcription	Esophagus	oesophagus
37	chr17:18242600-18258200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr17:18242600-18260400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr17:18242800-18257000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:18243600-18248600	Genic enhancers	Liver	Liver
41	chr17:18243600-18260400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr17:18243800-18264200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr17:18244000-18256200	Weak transcription	Colon Smooth Muscle	Colon
44	chr17:18244000-18263800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr17:18244200-18248200	Weak transcription	Ovary	ovary
46	chr17:18244200-18249400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr17:18244200-18250200	Weak transcription	Colonic Mucosa	Colon
48	chr17:18244200-18259800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr17:18244200-18263800	Strong transcription	Fetal Intestine Small	intestine
50	chr17:18244400-18248200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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