Variant report

Variant	rs11143951
Chromosome Location	chr9:71451982-71451983
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	chr9:71451909..71453715-chr9:71457092..71459544,2	K562	blood:

Variant related genes	Relation type
ENSG00000236733	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10448322	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10448338	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10781282	0.87[CEU][hapmap]
rs10869320	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10869538	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs11143691	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs11143715	0.82[CEU][hapmap]
rs11143741	0.87[CEU][hapmap]
rs11143761	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143777	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143870	0.87[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143882	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143900	0.82[CEU][hapmap]
rs11143938	0.92[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11143988	0.93[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144059	0.80[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs11144063	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144074	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144136	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144138	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144152	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144154	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144158	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144162	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144163	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144178	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144181	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144191	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144206	0.93[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes]
rs11144215	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144274	0.88[EUR][1000 genomes]
rs11144305	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]
rs11144327	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144351	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]
rs12003432	0.93[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs12339235	0.82[CEU][hapmap]
rs12376037	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12376991	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377033	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12379061	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12380573	1.00[MEX][hapmap]
rs12552102	0.86[CEU][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap]
rs12555680	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12555728	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs1414951	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414952	1.00[YRI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414954	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]
rs17057680	0.93[CEU][hapmap];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17058634	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17058780	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17058792	0.82[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs17391456	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17391582	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17483165	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4376559	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4623507	0.82[MEX][hapmap];0.91[MKK][hapmap]
rs4744737	1.00[ASN][1000 genomes]
rs62552132	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62566870	1.00[ASN][1000 genomes]
rs62566871	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62566872	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62566911	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62566915	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62566916	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62569347	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62569349	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62571161	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7018854	0.87[CEU][hapmap]
rs7024695	0.82[CEU][hapmap]
rs7035892	0.82[CEU][hapmap]
rs7042283	0.93[EUR][1000 genomes]
rs72717956	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72720053	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72720061	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72720068	0.95[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[EUR][1000 genomes]
rs950786	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032210	chr9:71130848-71511987	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv6548	chr9:71429527-71470917	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11143951	FAM189A2	cis	cerebellum	SCAN
rs11143951	TRPM3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71435800-71464800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:71437600-71453200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr9:71438000-71491200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:71439200-71456000	Weak transcription	GM12878-XiMat	blood
5	chr9:71440600-71466600	Weak transcription	Gastric	stomach
6	chr9:71441000-71478600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr9:71441600-71459800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr9:71443600-71458600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr9:71443600-71459000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr9:71445600-71454400	Weak transcription	Fetal Intestine Large	intestine
11	chr9:71445600-71458600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr9:71448200-71485600	Weak transcription	Stomach Mucosa	stomach
13	chr9:71448800-71455800	Weak transcription	Aorta	Aorta
14	chr9:71449200-71459200	Weak transcription	Primary B cells from cord blood	blood
15	chr9:71449600-71453200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr9:71449800-71456800	Weak transcription	Fetal Intestine Small	intestine
17	chr9:71450400-71453800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:71451000-71452000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr9:71451600-71452000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:71451600-71452000	Enhancers	Spleen	Spleen
21	chr9:71451600-71452200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:71451600-71455000	Enhancers	Fetal Heart	heart
23	chr9:71451800-71452200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr9:71451800-71452200	Enhancers	Fetal Kidney	kidney
25	chr9:71451800-71452200	Enhancers	Left Ventricle	heart
26	chr9:71451800-71452200	Enhancers	Lung	lung
27	chr9:71451800-71452200	Enhancers	Right Atrium	heart
28	chr9:71451800-71452200	Enhancers	Right Ventricle	heart
29	chr9:71451800-71453200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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