Variant report

Variant	rs1414954
Chromosome Location	chr9:71528163-71528164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71525845..71528360-chr9:71529223..71531031,2	MCF-7	breast:

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10448322	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10448338	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10781282	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs10869320	1.00[CEU][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10869538	0.93[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs11143691	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs11143715	0.82[CEU][hapmap]
rs11143741	0.87[CEU][hapmap]
rs11143761	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs11143777	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143870	0.87[CEU][hapmap];1.00[ASN][1000 genomes]
rs11143882	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143900	0.82[CEU][hapmap]
rs11143938	0.92[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143951	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143988	0.93[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144059	0.80[CEU][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11144063	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144074	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144136	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144138	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144152	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144154	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144158	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144162	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144163	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144178	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144181	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144191	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144206	0.93[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11144215	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144274	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11144305	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144327	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144351	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12003432	0.93[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12339235	0.82[CEU][hapmap]
rs12376037	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12376991	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377033	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12379061	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12380573	1.00[MEX][hapmap]
rs12552102	0.86[CEU][hapmap];0.82[MEX][hapmap]
rs12555680	1.00[ASN][1000 genomes]
rs12555728	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs1414951	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414952	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17057680	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs17058634	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17058780	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17058792	0.82[CEU][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs17391456	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs17391582	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17406856	1.00[LWK][hapmap]
rs17483165	1.00[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4376559	0.81[CEU][hapmap];1.00[ASN][1000 genomes]
rs4623507	0.82[MEX][hapmap]
rs4744737	1.00[ASN][1000 genomes]
rs62552132	1.00[ASN][1000 genomes]
rs62566870	1.00[ASN][1000 genomes]
rs62566871	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62566872	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62566911	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62566915	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62566916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62569347	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62569349	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62571161	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018854	0.87[CEU][hapmap]
rs7024695	0.82[CEU][hapmap]
rs7035892	0.82[CEU][hapmap]
rs7042283	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72717956	1.00[ASN][1000 genomes]
rs72720053	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72720061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72720068	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72722034	1.00[ASN][1000 genomes]
rs7865397	0.82[CEU][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs9411187	1.00[ASN][1000 genomes]
rs950786	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv466393	chr9:71453443-71704827	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv614547	chr9:71453443-71704827	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv614549	chr9:71506459-71659280	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv1051798	chr9:71511805-71792032	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1414954	TRPM3	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71510400-71576200	Weak transcription	Stomach Mucosa	stomach
2	chr9:71510600-71532400	Weak transcription	Small Intestine	intestine
3	chr9:71512200-71548800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:71514000-71532000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr9:71514200-71528600	Weak transcription	Left Ventricle	heart
6	chr9:71514200-71553600	Weak transcription	Aorta	Aorta
7	chr9:71514200-71557800	Weak transcription	Lung	lung
8	chr9:71514400-71532000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr9:71517400-71532400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr9:71519400-71573000	Weak transcription	Gastric	stomach
11	chr9:71520400-71530000	Weak transcription	Right Atrium	heart
12	chr9:71520400-71535400	Weak transcription	Fetal Intestine Small	intestine
13	chr9:71520600-71534000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:71521000-71534600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr9:71521200-71533800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr9:71522200-71528400	Weak transcription	Fetal Intestine Large	intestine
17	chr9:71527000-71528200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:71527200-71530400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr9:71527400-71528400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr9:71527400-71528600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:71527600-71528200	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr9:71527600-71528400	Enhancers	H9 Cell Line	embryonic stem cell
23	chr9:71527600-71528400	Strong transcription	Primary B cells from cord blood	blood
24	chr9:71527600-71528400	Enhancers	Duodenum Mucosa	Duodenum
25	chr9:71527600-71528400	Enhancers	Fetal Kidney	kidney
26	chr9:71527600-71528400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr9:71527600-71528400	Enhancers	GM12878-XiMat	blood
28	chr9:71527600-71528800	Enhancers	Pancreas	Pancrea
29	chr9:71527800-71528200	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr9:71527800-71528400	Enhancers	Colon Smooth Muscle	Colon
31	chr9:71528000-71528200	Enhancers	Fetal Heart	heart
32	chr9:71528000-71532400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:71528000-71542200	Weak transcription	Brain Angular Gyrus	brain

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