Variant report

Variant	rs10230356
Chromosome Location	chr7:69259613-69259614
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	chr7:69258902..69260777-chr7:69260844..69263060,2	MCF-7	breast:

Extended variants
information (count: 149 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs1000874	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10085600	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10215914	0.88[EUR][1000 genomes]
rs10216097	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10216186	0.85[EUR][1000 genomes]
rs10229336	0.85[EUR][1000 genomes]
rs10229578	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10229588	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10230750	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10233869	0.97[EUR][1000 genomes]
rs10234831	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10235098	0.85[EUR][1000 genomes]
rs10236103	1.00[EUR][1000 genomes]
rs10238307	0.97[EUR][1000 genomes]
rs10239569	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10240462	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10242206	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10243408	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10244001	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10244128	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10244247	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10244885	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10245690	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10245749	0.85[EUR][1000 genomes]
rs10247386	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10248237	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10254086	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10255563	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10256512	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10256943	0.97[EUR][1000 genomes]
rs10257587	0.97[EUR][1000 genomes]
rs10258846	0.85[EUR][1000 genomes]
rs10261380	0.97[EUR][1000 genomes]
rs10263467	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10268729	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10269267	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10272781	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10274099	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10274419	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10275112	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10275721	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10278001	0.85[EUR][1000 genomes]
rs10278978	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10279669	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10279708	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10452705	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10452739	0.85[EUR][1000 genomes]
rs10487943	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10950193	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11762049	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11762487	0.85[EUR][1000 genomes]
rs11763426	0.88[EUR][1000 genomes]
rs11764277	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11764717	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11769033	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11769738	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11770241	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11771751	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11771899	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11772602	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11975481	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11975506	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11979745	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12333653	0.85[EUR][1000 genomes]
rs17140755	0.97[EUR][1000 genomes]
rs17140759	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17140783	0.97[EUR][1000 genomes]
rs17140817	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17140884	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17140938	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17141032	0.85[EUR][1000 genomes]
rs17353920	0.84[EUR][1000 genomes]
rs17457910	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17458713	0.84[EUR][1000 genomes]
rs2052124	0.84[EUR][1000 genomes]
rs2068718	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28393394	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28493290	0.97[EUR][1000 genomes]
rs28496072	0.85[EUR][1000 genomes]
rs28502437	0.85[EUR][1000 genomes]
rs28577243	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2865804	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28812289	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28864527	0.85[EUR][1000 genomes]
rs34080361	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3735260	0.89[MEX][hapmap]
rs3800979	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41379648	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4305786	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55654955	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55756263	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55880824	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56405888	0.88[EUR][1000 genomes]
rs56800568	0.94[EUR][1000 genomes]
rs57493471	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58626042	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58666988	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58863846	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61370051	0.82[EUR][1000 genomes]
rs61424317	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6460525	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6945524	0.84[EUR][1000 genomes]
rs6947326	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6950638	0.97[EUR][1000 genomes]
rs6951770	1.00[EUR][1000 genomes]
rs6958450	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6958714	0.85[EUR][1000 genomes]
rs6962237	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6962338	0.84[EUR][1000 genomes]
rs6967788	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6968426	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6975211	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6977472	1.00[EUR][1000 genomes]
rs6978818	0.85[EUR][1000 genomes]
rs6980305	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs717266	0.97[EUR][1000 genomes]
rs719294	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73154605	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73164795	0.97[EUR][1000 genomes]
rs73166559	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73167506	0.97[EUR][1000 genomes]
rs73168739	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73168740	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73168747	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73168758	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73170834	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73170852	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73170857	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73170864	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73172903	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs740946	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7777243	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7777269	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7777621	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7780835	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7781664	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7784950	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7801209	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7810982	1.00[EUR][1000 genomes]
rs917718	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs917725	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9690738	0.85[EUR][1000 genomes]
rs9690769	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	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
6	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
rs10230356	CLDND2	trans	brain	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69247000-69264400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:69247200-69262200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:69249800-69269600	Weak transcription	Brain Angular Gyrus	brain
4	chr7:69250200-69261200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr7:69252400-69260400	Weak transcription	GM12878-XiMat	blood
6	chr7:69253400-69278800	Weak transcription	Fetal Stomach	stomach
7	chr7:69253600-69264600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr7:69254400-69265600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:69255000-69276600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:69255200-69262200	Weak transcription	Adipose Nuclei	Adipose
11	chr7:69256000-69265200	Weak transcription	Right Atrium	heart
12	chr7:69256600-69261000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:69256600-69264000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:69256800-69265000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr7:69257000-69265200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr7:69257200-69265800	Weak transcription	Brain Germinal Matrix	brain
17	chr7:69258600-69264400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:69259000-69269200	Weak transcription	Fetal Brain Male	brain
19	chr7:69259200-69261200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr7:69259200-69264400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr7:69259200-69265400	Weak transcription	Colon Smooth Muscle	Colon
22	chr7:69259400-69261000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr7:69259400-69264400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:69259400-69265400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr7:69259600-69259800	Enhancers	Ovary	ovary
26	chr7:69259600-69264400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr7:69259600-69264400	Weak transcription	Fetal Intestine Small	intestine
28	chr7:69259600-69264600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:69259600-69264600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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