Variant report

Variant	rs11951416
Chromosome Location	chr5:15688051-15688052
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10520821	0.80[AMR][1000 genomes]
rs10866514	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11133821	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11748790	0.90[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11750054	0.87[AMR][1000 genomes]
rs11950539	0.80[AMR][1000 genomes]
rs12152734	0.89[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12153463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12153747	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12519807	0.84[MKK][hapmap]
rs12659413	0.84[MKK][hapmap]
rs13180702	0.83[AMR][1000 genomes]
rs13358928	0.87[AMR][1000 genomes]
rs16867538	0.83[AMR][1000 genomes]
rs16867615	0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16867617	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2937074	0.85[AMR][1000 genomes]
rs2937075	1.00[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes]
rs34308971	0.87[AMR][1000 genomes]
rs35167698	0.87[AMR][1000 genomes]
rs35719201	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4146556	1.00[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes]
rs4235553	0.81[LWK][hapmap]
rs4235554	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4235555	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4273602	0.84[MKK][hapmap]
rs4273604	0.87[AMR][1000 genomes]
rs4312881	0.86[AMR][1000 genomes]
rs4318779	0.84[AMR][1000 genomes]
rs4484432	0.89[CEU][hapmap];0.86[AMR][1000 genomes]
rs4568364	0.84[CHB][hapmap];0.87[AMR][1000 genomes]
rs4574543	0.87[AMR][1000 genomes]
rs4576146	0.87[AMR][1000 genomes]
rs4601044	0.81[AMR][1000 genomes]
rs4701638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4701639	0.89[CEU][hapmap];0.83[CHB][hapmap];0.84[AMR][1000 genomes]
rs4701641	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4702100	0.86[LWK][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap]
rs4702102	0.89[CEU][hapmap];0.85[CHB][hapmap];0.80[EUR][1000 genomes]
rs4702103	0.92[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6554897	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6862949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6885069	0.81[LWK][hapmap];0.81[AMR][1000 genomes]
rs6892021	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6892414	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7704590	0.89[LWK][hapmap];0.84[MKK][hapmap]
rs7732283	0.81[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530222	chr5:15151662-15851485	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv830214	chr5:15589809-15791032	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3507774	chr5:15593461-15822407	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3507776	chr5:15593461-15822407	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1028089	chr5:15636285-15883910	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv537676	chr5:15636285-15883910	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1024248	chr5:15638067-15863583	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv537677	chr5:15638067-15863583	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv880755	chr5:15670377-15938553	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
13	nsv597263	chr5:15672137-15720478	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv461983	chr5:15674635-15720106	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv597264	chr5:15674635-15720106	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv2757107	chr5:15678556-15810987	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv2759327	chr5:15678556-15810987	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11951416	TIMP3	trans	parietal	SCAN
rs11951416	SLC23A3	trans	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15675200-15693000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:15677000-15690800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:15682400-15690800	Weak transcription	Aorta	Aorta
4	chr5:15683600-15689000	Weak transcription	Left Ventricle	heart
5	chr5:15683800-15688600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:15684000-15695200	Weak transcription	HUVEC	blood vessel
7	chr5:15684200-15689000	Weak transcription	Lung	lung
8	chr5:15684600-15691200	Weak transcription	Fetal Stomach	stomach
9	chr5:15684600-15694000	Weak transcription	Fetal Kidney	kidney
10	chr5:15684800-15693000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:15685000-15689400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:15685000-15690000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:15685000-15690000	Weak transcription	HSMMtube	muscle
14	chr5:15685000-15690200	Weak transcription	NHDF-Ad	bronchial
15	chr5:15686200-15688800	Enhancers	Brain Hippocampus Middle	brain
16	chr5:15686400-15690800	Weak transcription	Ovary	ovary
17	chr5:15686600-15688200	Enhancers	Brain Cingulate Gyrus	brain
18	chr5:15686600-15690200	Weak transcription	Colon Smooth Muscle	Colon
19	chr5:15686600-15694400	Weak transcription	Fetal Lung	lung
20	chr5:15687000-15688400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:15687000-15689000	Enhancers	Brain Substantia Nigra	brain
22	chr5:15687200-15688200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:15687200-15688200	Enhancers	Brain Angular Gyrus	brain
24	chr5:15687200-15688400	Weak transcription	Fetal Heart	heart
25	chr5:15687200-15688600	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr5:15687400-15688200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:15687600-15690800	Weak transcription	Right Ventricle	heart
28	chr5:15687800-15690800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:15687800-15690800	Weak transcription	Right Atrium	heart
30	chr5:15687800-15691000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr5:15687800-15691200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:15687800-15691200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr5:15687800-15691200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:15687800-15691400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr5:15687800-15694200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr5:15687800-15694200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:15688000-15690800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr5:15688000-15690800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr5:15688000-15690800	Weak transcription	Brain Anterior Caudate	brain
40	chr5:15688000-15694200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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