Variant report

Variant	rs10865398
Chromosome Location	chr2:73741497-73741498
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	chr2:73611808..73614254-chr2:73740425..73742258,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116127	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10165862	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs10189578	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10190002	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10207970	0.81[EUR][1000 genomes]
rs1052161	0.96[CEU][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs1083919	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1083920	0.84[ASN][1000 genomes]
rs1083921	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1083922	0.81[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1083923	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1091568	0.86[ASN][1000 genomes]
rs11126399	1.00[CHB][hapmap]
rs11126402	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11126414	0.82[GIH][hapmap];0.84[TSI][hapmap]
rs11685372	0.87[ASN][1000 genomes]
rs11688718	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11689767	0.82[ASN][1000 genomes]
rs12233112	0.93[YRI][hapmap]
rs1246094	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1246096	0.84[ASN][1000 genomes]
rs1246105	0.84[ASN][1000 genomes]
rs12465867	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs12618600	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap]
rs12620018	0.96[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap]
rs12620091	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs12991161	0.96[CEU][hapmap]
rs12995433	0.89[EUR][1000 genomes]
rs12996463	0.90[EUR][1000 genomes]
rs13009035	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13017182	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs13027816	0.96[CEU][hapmap]
rs1320374	0.83[ASW][hapmap];0.96[CEU][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs13386124	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13399087	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1403412	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs1406105	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs1528169	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1852647	1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1881246	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1881247	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2017116	1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs2037814	1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap]
rs2091503	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2091504	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2178154	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2421489	0.92[CHB][hapmap]
rs2421545	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2421546	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2421548	0.89[EUR][1000 genomes]
rs2421574	0.88[CEU][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs2421581	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs2421582	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2421583	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]
rs2421586	0.96[CEU][hapmap];0.87[GIH][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap]
rs2421667	0.84[EUR][1000 genomes]
rs2421668	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap]
rs2421669	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs2948441	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs3820700	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs4346412	0.85[EUR][1000 genomes]
rs4511748	0.92[CHB][hapmap]
rs4852305	0.81[JPT][hapmap]
rs4852306	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4852308	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4852927	0.88[EUR][1000 genomes]
rs4852951	0.95[CEU][hapmap]
rs4852954	0.88[CEU][hapmap];0.82[GIH][hapmap];0.85[MKK][hapmap]
rs4852959	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap]
rs4852975	0.82[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap]
rs4852976	0.82[GIH][hapmap];0.91[MEX][hapmap];0.93[YRI][hapmap]
rs55677218	0.87[ASN][1000 genomes]
rs56054150	0.82[ASN][1000 genomes]
rs56068325	0.84[ASN][1000 genomes]
rs56770679	0.88[ASN][1000 genomes]
rs62153184	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6546826	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs6546827	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs6546829	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6546830	0.82[ASN][1000 genomes]
rs6546832	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs6546842	0.92[ASN][1000 genomes]
rs6546846	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6546870	0.92[CHB][hapmap]
rs66931335	0.83[ASN][1000 genomes]
rs6706235	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6706409	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap]
rs6710659	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6722867	0.89[EUR][1000 genomes]
rs6729468	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6730785	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6732440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs6742619	0.87[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]
rs6743576	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6744697	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6745560	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6746971	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6747145	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap]
rs6748040	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs6749680	1.00[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6757996	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67877078	0.84[ASN][1000 genomes]
rs67898050	0.92[ASN][1000 genomes]
rs68154245	0.93[ASN][1000 genomes]
rs72811933	0.84[ASN][1000 genomes]
rs72811939	0.85[ASN][1000 genomes]
rs7562047	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7566315	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7570683	0.96[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap]
rs7574291	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs7576824	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap]
rs7585119	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7598660	0.92[CEU][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs7598901	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7606483	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7606947	0.88[CEU][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs7608308	0.84[ASN][1000 genomes]
rs7609249	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs780388	0.88[ASN][1000 genomes]
rs780389	0.88[ASN][1000 genomes]
rs780390	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs780391	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs780393	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs780394	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs780395	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs780396	1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs802113	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428051	chr2:73717032-74030067	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv874267	chr2:73717656-73857002	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10865398	MXD1	cis	cerebellum	SCAN
rs10865398	DUSP11	cis	parietal	SCAN
rs10865398	ALMS1P	cis	cerebellum	SCAN
rs10865398	ALMS1P	cis	parietal	SCAN
rs10865398	ALMS1	cis	parietal	SCAN
rs10865398	LRRTM4	cis	cerebellum	SCAN
rs10865398	ALMS1	cis	cerebellum	SCAN
rs10865398	DUSP11	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73713200-73757400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:73715600-73751800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:73717400-73757800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:73718000-73746800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:73719400-73747000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr2:73728200-73747000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:73731600-73759000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:73731800-73746800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:73731800-73752000	Weak transcription	Fetal Heart	heart
10	chr2:73731800-73807600	Weak transcription	Hela-S3	cervix
11	chr2:73735600-73743000	Weak transcription	Fetal Intestine Large	intestine
12	chr2:73736400-73761600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:73736800-73747400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:73737600-73744000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:73737600-73747400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:73737600-73750600	Weak transcription	Small Intestine	intestine
17	chr2:73738000-73746800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:73738600-73746800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:73738800-73750200	Weak transcription	Stomach Mucosa	stomach
20	chr2:73739400-73756400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:73739800-73742800	ZNF genes & repeats	Dnd41	blood
22	chr2:73740000-73747000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:73740200-73742200	ZNF genes & repeats	HSMM	muscle
24	chr2:73740400-73741600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:73740600-73746800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:73740600-73747000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:73740600-73747000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:73740800-73744400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:73740800-73747400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:73740800-73752600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:73740800-73752800	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:73740800-73753800	Weak transcription	Brain Angular Gyrus	brain
33	chr2:73740800-73757600	Weak transcription	Ovary	ovary
34	chr2:73741000-73742600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr2:73741000-73747000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:73741000-73747000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:73741000-73748400	Weak transcription	Fetal Lung	lung
38	chr2:73741000-73748800	Weak transcription	Esophagus	oesophagus
39	chr2:73741000-73749200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:73741000-73750200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:73741000-73751000	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:73741000-73751800	Weak transcription	Fetal Kidney	kidney
43	chr2:73741000-73752200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:73741000-73752200	Weak transcription	Brain Substantia Nigra	brain
45	chr2:73741000-73752200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:73741000-73752600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:73741000-73755000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:73741000-73755600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr2:73741000-73756200	Weak transcription	Fetal Intestine Small	intestine
50	chr2:73741000-73756400	Weak transcription	Thymus	Thymus

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