Variant report

Variant	rs9405807
Chromosome Location	chr6:5162376-5162377
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1055415	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12206736	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1535041	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1570085	1.00[JPT][hapmap]
rs17139748	0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1970010	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2145372	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2224391	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2746220	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2746221	0.95[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2746222	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2746226	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2746243	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2753230	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2753235	1.00[JPT][hapmap]
rs2753237	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2753238	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2753239	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2753244	1.00[JPT][hapmap]
rs2753245	1.00[JPT][hapmap]
rs2753246	1.00[JPT][hapmap]
rs2753248	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2753255	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs2773287	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2773289	0.85[EUR][1000 genomes]
rs2773294	0.91[CEU][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs2773296	0.91[CEU][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs2773311	1.00[JPT][hapmap]
rs2773314	1.00[JPT][hapmap]
rs2773316	1.00[JPT][hapmap]
rs2773317	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2773318	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2773319	1.00[JPT][hapmap]
rs2773333	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2773336	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2773337	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2773339	0.84[EUR][1000 genomes]
rs35943326	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs367803	0.91[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs374253	0.81[EUR][1000 genomes]
rs391313	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs393391	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs393454	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs399283	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap]
rs409295	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs416803	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs419778	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs421186	0.82[EUR][1000 genomes]
rs421720	0.91[CEU][hapmap];0.94[JPT][hapmap]
rs4246073	0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs429031	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs429490	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs434450	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs439356	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs445711	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs447604	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4960074	0.95[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs761359	0.84[EUR][1000 genomes]
rs761360	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs761361	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9328289	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes]
rs9378943	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9392664	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9392665	0.87[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs9405809	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9504356	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9504370	0.82[CHD][hapmap];1.00[JPT][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	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1034681	chr6:5070351-5387176	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv538113	chr6:5070351-5387176	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS 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	15 gene(s)	inside rSNPs	diseases
8	nsv1018152	chr6:5077025-5387176	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv600873	chr6:5089278-5400658	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats 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 miRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1017821	chr6:5114609-5213200	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
11	nsv538114	chr6:5114609-5213200	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	5 gene(s)	inside rSNPs	diseases
12	nsv5179	chr6:5121824-5167027	Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1030254	chr6:5132261-5431585	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
14	nsv1034463	chr6:5137959-5345678	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
15	nsv1022336	chr6:5145194-5200687	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
16	nsv1018984	chr6:5145194-5200801	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
17	nsv1021646	chr6:5157795-5367254	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats 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	8 gene(s)	inside rSNPs	diseases
18	nsv538115	chr6:5157795-5367254	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers 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	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9405807	LYRM4	cis	parietal	SCAN
rs9405807	FARS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5130600-5172200	Weak transcription	Lung	lung
2	chr6:5137000-5166600	Weak transcription	Primary T cells from cord blood	blood
3	chr6:5143600-5172400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:5144000-5175400	Weak transcription	HepG2	liver
5	chr6:5145400-5180800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:5153000-5162600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:5153000-5163200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:5153200-5178200	Weak transcription	HMEC	breast
9	chr6:5156000-5171000	Weak transcription	Fetal Kidney	kidney
10	chr6:5158400-5164200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:5158600-5174000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:5159600-5164000	Weak transcription	Pancreas	Pancrea
13	chr6:5159800-5174000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:5160200-5172200	Weak transcription	NHEK	skin
15	chr6:5162000-5162800	Enhancers	K562	blood
16	chr6:5162000-5163000	Enhancers	Primary hematopoietic stem cells	blood
17	chr6:5162200-5162400	Enhancers	Fetal Brain Female	brain
18	chr6:5162200-5162400	Enhancers	Placenta	Placenta
19	chr6:5162200-5164200	Enhancers	Fetal Brain Male	brain

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