Variant report

Variant	rs17140817
Chromosome Location	chr7:69161095-69161096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 143 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs1000874	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10085600	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10216097	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10216186	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10229336	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10229578	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229588	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10230356	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10230750	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233869	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10234831	0.83[EUR][1000 genomes]
rs10236103	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10238307	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10239569	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10240462	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10242206	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10243408	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10244001	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10244128	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10244247	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10244885	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10245690	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10247386	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10248237	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254086	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10255563	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10256309	0.90[AMR][1000 genomes]
rs10256512	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10256943	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10257587	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10258846	0.87[EUR][1000 genomes]
rs10261380	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10263467	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10268729	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10269267	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10272781	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10274099	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10274419	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10275112	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10275721	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10278978	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10279669	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10279708	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10280018	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10452705	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10487943	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10950193	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11762049	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11762487	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11764277	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11764717	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769033	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11769738	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11770241	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11771751	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11771899	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11772602	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11975481	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11975506	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11979745	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17140755	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17140759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17140783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17140884	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17140938	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17141032	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17350805	0.80[EUR][1000 genomes]
rs17353920	0.87[EUR][1000 genomes]
rs17457910	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17458713	0.87[EUR][1000 genomes]
rs2052124	0.87[EUR][1000 genomes]
rs2068718	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28393394	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28493290	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28577243	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2865804	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28812289	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34080361	0.93[EUR][1000 genomes]
rs3735260	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[ASN][1000 genomes]
rs3800979	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41379648	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4305786	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55654955	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55756263	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55880824	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56800568	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57493471	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58626042	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58666988	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58863846	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61370051	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61424317	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61744589	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6460525	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945524	0.87[EUR][1000 genomes]
rs6947326	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6950638	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6951770	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6958450	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6958714	0.87[EUR][1000 genomes]
rs6962237	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6962338	0.87[EUR][1000 genomes]
rs6967788	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6968426	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6975211	0.87[EUR][1000 genomes]
rs6977472	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6980305	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs717266	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs719294	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73154605	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73164795	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166559	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73167506	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73168739	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73168740	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73168747	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73168758	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73170834	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170852	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73170857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73170864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73172903	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs740946	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7777243	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7777269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7777621	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7780835	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7781664	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7784950	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7801209	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7810982	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs917718	0.87[EUR][1000 genomes]
rs917725	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9690738	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9690769	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[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	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv428169	chr7:69021482-69196743	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv831021	chr7:69122169-69364491	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1021538	chr7:69130236-69575753	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv538917	chr7:69130236-69575753	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv817276	chr7:69130237-69736834	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1034380	chr7:69137914-69171449	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
8	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17140817	CLDND2	trans	brain	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69148400-69166200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:69150200-69161400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr7:69150600-69162600	Weak transcription	Colon Smooth Muscle	Colon
4	chr7:69151200-69161200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:69153400-69161200	Weak transcription	Brain Germinal Matrix	brain
6	chr7:69153400-69161200	Weak transcription	Fetal Brain Female	brain
7	chr7:69153600-69167400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:69156600-69166600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr7:69156800-69166400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr7:69157200-69167800	Weak transcription	Fetal Stomach	stomach
11	chr7:69159200-69167800	Weak transcription	Fetal Lung	lung
12	chr7:69159400-69163600	Enhancers	Fetal Thymus	thymus
13	chr7:69160000-69162000	Enhancers	Primary B cells from cord blood	blood
14	chr7:69160000-69162600	Enhancers	Thymus	Thymus
15	chr7:69160000-69162800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr7:69160200-69162600	Enhancers	Primary hematopoietic stem cells	blood
17	chr7:69160800-69161200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr7:69160800-69161400	Enhancers	Primary T cells fromperipheralblood	blood
19	chr7:69160800-69161400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr7:69160800-69161600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr7:69160800-69161600	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr7:69160800-69161600	Flanking Active TSS	GM12878-XiMat	blood
23	chr7:69160800-69161800	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr7:69160800-69161800	Flanking Active TSS	Dnd41	blood
25	chr7:69160800-69162000	Enhancers	Primary T cells from cord blood	blood
26	chr7:69160800-69162200	Enhancers	Primary B cells from peripheral blood	blood
27	chr7:69160800-69162800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr7:69161000-69161200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr7:69161000-69161400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:69161000-69161400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:69161000-69161400	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr7:69161000-69161400	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr7:69161000-69161400	Enhancers	Fetal Muscle Leg	muscle
34	chr7:69161000-69161400	Enhancers	Left Ventricle	heart
35	chr7:69161000-69161600	Enhancers	Adipose Nuclei	Adipose
36	chr7:69161000-69161600	Enhancers	Brain Anterior Caudate	brain
37	chr7:69161000-69161600	Enhancers	Right Atrium	heart
38	chr7:69161000-69161800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:69161000-69161800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr7:69161000-69161800	Enhancers	Fetal Brain Male	brain
41	chr7:69161000-69162000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr7:69161000-69162200	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr7:69161000-69162600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:69161000-69164200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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