Variant report

Variant	rs9961669
Chromosome Location	chr18:13020881-13020882
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:13017737..13019415-chr18:13020014..13022473,2	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10221326	0.92[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10221384	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11080620	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11663049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12605081	0.80[CEU][hapmap]
rs12605638	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12954256	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12955780	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1474043	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1786263	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1786270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1786279	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1787000	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1787003	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1787004	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1787008	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1973779	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28619103	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28641764	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2902856	0.82[CEU][hapmap];0.83[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35790309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3809912	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs472702	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs472992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs473580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs474337	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475139	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs478006	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs478399	0.86[EUR][1000 genomes]
rs482360	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs482577	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs490853	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs491349	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs492723	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs498685	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4995995	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs518145	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs527839	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs547084	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs554719	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs554854	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs556371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs556536	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs557846	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs562151	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs565832	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs567031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs569453	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs570505	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs576963	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs578208	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6505774	0.82[CEU][hapmap]
rs6505775	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6505777	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6505780	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs692833	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs692964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71353243	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7226616	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7229870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7233600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7233814	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7234094	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7234960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7236162	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7236764	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7237236	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7241536	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7243660	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8088313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8089123	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8097038	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8097125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9783859	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9783903	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9948139	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9948681	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9949589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9949682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9951698	0.81[AMR][1000 genomes]
rs9952698	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9958369	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9964466	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription 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 lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1062413	chr18:12988947-13039941	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv543657	chr18:12988947-13039941	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs9961669	CEP192	cis	Temporal Cortex	GTEx
rs9961669	CEP192	cis	Esophagus Muscularis	GTEx
rs9961669	CEP192	cis	Thyroid	GTEx
rs9961669	CEP192	cis	Esophagus Mucosa	GTEx
rs9961669	CEP192	cis	Whole Blood	GTEx
rs9961669	CEP192	cis	Skin Sun Exposed Lower leg	GTEx
rs9961669	CEP192	cis	Stomach	GTEx
rs9961669	CEP192	cis	Adipose Subcutaneous	GTEx
rs9961669	CEP192	cis	multi-tissue	Pritchard
rs9961669	CEP192	cis	Artery Tibial	GTEx
rs9961669	CEP192	cis	Nerve Tibial	GTEx
rs9961669	CEP192	cis	Artery Aorta	GTEx
rs9961669	CEP192	cis	Brain Pons	GTEx
rs9961669	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs9961669	CEP192	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12992600-13031200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr18:12993000-13023800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr18:12995200-13042000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr18:12998400-13041600	Strong transcription	Dnd41	blood
5	chr18:12999200-13039000	Strong transcription	Fetal Thymus	thymus
6	chr18:12999400-13021800	Strong transcription	Primary T cells from cord blood	blood
7	chr18:13000400-13034000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr18:13002800-13021200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr18:13004800-13024200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr18:13004800-13031800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr18:13005000-13039200	Strong transcription	Primary B cells from peripheral blood	blood
12	chr18:13005400-13033400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr18:13006400-13034400	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr18:13007200-13044000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr18:13007800-13021000	Strong transcription	Liver	Liver
16	chr18:13007800-13022400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr18:13008000-13022000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr18:13008000-13025000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr18:13008000-13046000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr18:13008200-13021200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr18:13008400-13021000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr18:13008400-13021000	Strong transcription	Adipose Nuclei	Adipose
23	chr18:13008400-13021800	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr18:13008400-13022400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr18:13008400-13047200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr18:13008600-13022600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr18:13011200-13021200	Strong transcription	Fetal Muscle Leg	muscle
28	chr18:13011200-13022000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr18:13011400-13021800	Strong transcription	K562	blood
30	chr18:13011400-13022600	Strong transcription	Primary hematopoietic stem cells	blood
31	chr18:13011400-13034000	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr18:13011400-13038800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr18:13011800-13023400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr18:13011800-13024200	Strong transcription	HSMM	muscle
35	chr18:13011800-13033800	Strong transcription	Primary B cells from cord blood	blood
36	chr18:13013600-13025600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr18:13013800-13031800	Weak transcription	Pancreas	Pancrea
38	chr18:13013800-13052000	Weak transcription	Right Ventricle	heart
39	chr18:13013800-13053200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr18:13014200-13029800	Weak transcription	Colonic Mucosa	Colon
41	chr18:13014200-13047200	Weak transcription	Psoas Muscle	Psoas
42	chr18:13014800-13021000	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr18:13015400-13036400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr18:13015600-13048800	Weak transcription	Small Intestine	intestine
45	chr18:13016400-13024800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr18:13016400-13027000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr18:13016400-13036200	Weak transcription	Gastric	stomach
48	chr18:13016600-13024800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr18:13016600-13031800	Weak transcription	Spleen	Spleen
50	chr18:13016800-13024800	Weak transcription	Fetal Stomach	stomach

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