Variant report

Variant	rs497331
Chromosome Location	chr10:97370331-97370332
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97368105..97370562-chr10:97374316..97376583,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000059573	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10159941	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs10509687	1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10748634	0.92[CHB][hapmap]
rs10748635	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10748636	0.86[ASN][1000 genomes]
rs10748637	0.92[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs10786228	0.84[CHB][hapmap]
rs10786230	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs10786235	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs10786238	0.81[AFR][1000 genomes]
rs10882646	0.92[CHB][hapmap]
rs10882653	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs10882664	0.85[CHB][hapmap]
rs10882665	0.85[CHB][hapmap]
rs11188414	0.84[CHB][hapmap]
rs11188441	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11188459	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs11188485	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs11188488	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes]
rs11596004	0.82[CHB][hapmap]
rs12262943	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1340837	0.93[JPT][hapmap];0.95[YRI][hapmap]
rs17111041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890187	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1933166	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs1933169	0.84[CHB][hapmap]
rs1953710	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs2211002	0.92[CHB][hapmap]
rs2225892	0.85[ASN][1000 genomes]
rs2225893	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2275273	0.85[CHB][hapmap]
rs3750700	0.85[CHB][hapmap]
rs3750701	0.85[CHB][hapmap]
rs3763705	0.84[ASN][1000 genomes]
rs3763706	0.86[ASN][1000 genomes]
rs3793748	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs3949478	0.85[CHB][hapmap]
rs4290159	0.91[CHB][hapmap]
rs4457685	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs4501930	0.85[CHB][hapmap]
rs473251	0.86[ASN][1000 genomes]
rs476373	0.83[ASN][1000 genomes]
rs482811	0.82[ASN][1000 genomes]
rs4917698	0.86[ASN][1000 genomes]
rs4918950	0.92[CHB][hapmap]
rs4918956	0.86[ASN][1000 genomes]
rs4918964	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs496426	0.92[CHB][hapmap]
rs501603	1.00[JPT][hapmap]
rs524084	0.87[ASN][1000 genomes]
rs556869	0.85[ASN][1000 genomes]
rs571505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6584026	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs6584028	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs7069234	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs7073723	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs7073936	0.84[ASN][1000 genomes]
rs7081414	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs7084741	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7085059	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7894052	0.86[ASN][1000 genomes]
rs7905653	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs7909569	0.92[CHB][hapmap]
rs7915345	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs7918235	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7920850	0.92[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs945958	0.92[CHB][hapmap]
rs951418	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526180	chr10:97332195-97511037	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs497331	TCTN3	cis	lymphoblastoid	seeQTL
rs497331	ENTPD1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97335200-97373400	Weak transcription	Psoas Muscle	Psoas
2	chr10:97363400-97370400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr10:97363400-97370400	Strong transcription	Fetal Intestine Small	intestine
4	chr10:97364000-97382000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr10:97364000-97409200	Strong transcription	Primary T cells from cord blood	blood
6	chr10:97364000-97411000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr10:97364200-97372000	Strong transcription	Fetal Intestine Large	intestine
8	chr10:97364400-97373200	Strong transcription	Liver	Liver
9	chr10:97364400-97378600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr10:97364400-97378600	Strong transcription	Fetal Brain Female	brain
11	chr10:97364400-97378600	Strong transcription	Spleen	Spleen
12	chr10:97364400-97379000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr10:97364400-97403200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr10:97364600-97372800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr10:97364600-97377400	Strong transcription	Placenta	Placenta
16	chr10:97364600-97378600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr10:97364600-97378600	Strong transcription	Pancreas	Pancrea
18	chr10:97364600-97378800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr10:97364600-97378800	Strong transcription	NH-A	brain
20	chr10:97364600-97379000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:97364600-97379000	Strong transcription	GM12878-XiMat	blood
22	chr10:97364600-97388400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr10:97364800-97372200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr10:97364800-97372600	Strong transcription	HepG2	liver
25	chr10:97364800-97378600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr10:97364800-97378600	Strong transcription	Gastric	stomach
27	chr10:97364800-97378800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:97364800-97378800	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr10:97364800-97378800	Strong transcription	Osteobl	bone
30	chr10:97364800-97379000	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr10:97364800-97403400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr10:97364800-97411000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr10:97365000-97372400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr10:97365000-97372400	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr10:97365000-97373600	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr10:97365000-97378200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr10:97365000-97378400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr10:97365000-97378600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr10:97365000-97378600	Strong transcription	Brain Germinal Matrix	brain
40	chr10:97365000-97378800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr10:97365000-97378800	Strong transcription	Adipose Nuclei	Adipose
42	chr10:97365000-97379000	Strong transcription	Dnd41	blood
43	chr10:97365000-97403000	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr10:97365000-97403400	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr10:97365200-97371800	Strong transcription	Ovary	ovary
46	chr10:97365200-97377800	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr10:97365200-97378600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr10:97365200-97378800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr10:97365200-97378800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr10:97365200-97379000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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