Variant report

Variant	rs200863
Chromosome Location	chr6:5143105-5143106
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs127124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs127125	0.90[ASN][1000 genomes]
rs200848	0.84[EUR][1000 genomes]
rs200849	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs364886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs376334	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs385315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs402541	0.96[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs412628	0.92[ASN][1000 genomes]
rs423801	0.92[ASN][1000 genomes]
rs435175	0.82[ASN][1000 genomes]
rs438298	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs445204	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449200	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs454984	0.92[ASN][1000 genomes]
rs455803	0.90[ASN][1000 genomes]
rs457453	0.88[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs457759	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs457846	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs461698	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs462749	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs464606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs464681	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs464863	0.90[ASN][1000 genomes]
rs466837	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs587777	0.88[ASN][1000 genomes]
rs683261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs85204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9606	0.96[CEU][hapmap];0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs200863	LYRM4	cis	multi-tissue	Pritchard
rs200863	LYRM4	Cis_1M	lymphoblastoid	RTeQTL
rs200863	C6orf149	cis	lesional skin	skin_eQTL

Chromatin state (count:34 , 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	chr6:5133400-5143200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:5133400-5143800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:5133400-5144000	Weak transcription	Fetal Brain Male	brain
6	chr6:5133400-5146000	Weak transcription	Psoas Muscle	Psoas
7	chr6:5133400-5151600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:5133600-5143400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:5133600-5143800	Weak transcription	Fetal Stomach	stomach
10	chr6:5133800-5143400	Weak transcription	Left Ventricle	heart
11	chr6:5133800-5143600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:5133800-5153400	Weak transcription	Right Ventricle	heart
13	chr6:5134200-5144200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr6:5135000-5151000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:5135200-5151800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:5136400-5151000	Weak transcription	NHEK	skin
17	chr6:5136400-5151600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:5137000-5166600	Weak transcription	Primary T cells from cord blood	blood
19	chr6:5139600-5143200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:5139800-5144200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:5140000-5143400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:5140000-5143800	Weak transcription	Fetal Kidney	kidney
23	chr6:5140000-5144200	Weak transcription	Fetal Lung	lung
24	chr6:5140000-5148600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:5140400-5143200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr6:5141000-5149200	Weak transcription	Primary B cells from cord blood	blood
27	chr6:5141600-5143600	Weak transcription	HepG2	liver
28	chr6:5141600-5144000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:5141800-5143200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:5141800-5143800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr6:5143000-5143200	Weak transcription	Fetal Intestine Small	intestine
32	chr6:5143000-5143200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
33	chr6:5143000-5143200	Enhancers	Spleen	Spleen
34	chr6:5143000-5144600	Enhancers	Fetal Muscle Leg	muscle

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