Variant report

Variant	rs2143693
Chromosome Location	chr6:5150703-5150704
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5149373..5152322-chr6:5189165..5191119,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1571564	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs175596	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs200859	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs200862	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs200866	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs200867	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[ASN][1000 genomes]
rs200868	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs200870	0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2746235	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2746239	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs399120	0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[ASN][1000 genomes]
rs424006	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs450176	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs458743	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs460416	1.00[JPT][hapmap]
rs460440	0.95[MEX][hapmap]
rs462327	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs462487	1.00[JPT][hapmap]
rs465481	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs466285	0.88[JPT][hapmap]
rs4960069	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs52401	0.82[ASN][1000 genomes]
rs6597117	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs7752848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7766717	0.91[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][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	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	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2143693	LYRM4	cis	lymphoblastoid	seeQTL
rs2143693	LYRM4	cis	Thyroid	GTEx
rs2143693	TUBB2B	cis	cerebellum	SCAN
rs2143693	LYRM4	cis	parietal	SCAN
rs2143693	LYRM4	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5129000-5162000	Weak transcription	K562	blood
2	chr6:5130600-5172200	Weak transcription	Lung	lung
3	chr6:5133400-5151600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:5133800-5153400	Weak transcription	Right Ventricle	heart
5	chr6:5135000-5151000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:5135200-5151800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:5136400-5151000	Weak transcription	NHEK	skin
8	chr6:5136400-5151600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:5137000-5166600	Weak transcription	Primary T cells from cord blood	blood
10	chr6:5143600-5152400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:5143600-5172400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:5144000-5152400	Weak transcription	Spleen	Spleen
13	chr6:5144000-5152800	Weak transcription	Left Ventricle	heart
14	chr6:5144000-5175400	Weak transcription	HepG2	liver
15	chr6:5144400-5151800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:5144400-5152800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:5144400-5157200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:5144600-5152400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:5145400-5180800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:5145600-5156600	Weak transcription	Fetal Stomach	stomach
21	chr6:5147000-5151000	Weak transcription	HMEC	breast
22	chr6:5147200-5151800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:5147400-5151600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:5147400-5151600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:5147400-5158000	Weak transcription	Primary hematopoietic stem cells	blood

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