Variant report

Variant	rs16890842
Chromosome Location	chr6:80258505-80258506
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	chr6:80246209..80248851-chr6:80258293..80260722,2	K562	blood:

Variant related genes	Relation type
ENSG00000135338	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10484941	0.89[MEX][hapmap]
rs11753205	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11756302	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11756486	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11757993	0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11758791	0.87[AFR][1000 genomes]
rs1472729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890791	0.92[CHD][hapmap]
rs16890821	0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs16890846	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1857722	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047897	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2069304	1.00[CEU][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2455943	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455944	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655665	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2655686	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655693	0.81[CEU][hapmap]
rs2803172	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803176	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803177	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803178	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803179	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803180	0.83[ASN][1000 genomes]
rs2812697	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2812699	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34068461	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4706790	0.85[JPT][hapmap]
rs4706791	0.85[JPT][hapmap]
rs4706792	0.81[CHB][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs55697211	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55951062	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56311322	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72899942	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs72899955	0.84[AMR][1000 genomes]
rs72901812	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72901839	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7743617	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7755562	0.85[JPT][hapmap]
rs7771276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774418	1.00[CEU][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7775536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9448733	0.85[AMR][1000 genomes]
rs9448738	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv886301	chr6:80111104-80339088	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv830707	chr6:80134625-80325171	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1029259	chr6:80142754-80340332	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv463906	chr6:80240951-80313297	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv604052	chr6:80240951-80313297	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1018318	chr6:80241029-80465282	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16890842	LCA5	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80247600-80267800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:80248000-80262000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:80248600-80262800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:80248600-80262800	Weak transcription	Liver	Liver
5	chr6:80248800-80262000	Weak transcription	Psoas Muscle	Psoas
6	chr6:80248800-80272000	Weak transcription	Ovary	ovary
7	chr6:80249400-80262200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:80254400-80262200	Weak transcription	Placenta	Placenta
9	chr6:80254400-80267800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:80254400-80271400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:80254400-80273000	Weak transcription	Left Ventricle	heart
12	chr6:80254600-80260000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:80254600-80273800	Weak transcription	Stomach Mucosa	stomach
14	chr6:80254800-80262000	Weak transcription	Right Ventricle	heart
15	chr6:80255000-80261600	Weak transcription	HepG2	liver
16	chr6:80255000-80280000	Weak transcription	Aorta	Aorta
17	chr6:80255200-80258800	Weak transcription	Brain Germinal Matrix	brain
18	chr6:80255200-80262600	Weak transcription	Fetal Brain Male	brain
19	chr6:80255200-80264800	Weak transcription	Fetal Heart	heart
20	chr6:80255200-80267800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:80255400-80260000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:80255400-80261600	Weak transcription	NHLF	lung
23	chr6:80255600-80260200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:80255600-80260200	Weak transcription	Fetal Brain Female	brain
25	chr6:80255600-80262200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:80255600-80264800	Weak transcription	Fetal Intestine Large	intestine
27	chr6:80255600-80279400	Weak transcription	HMEC	breast
28	chr6:80255600-80280000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr6:80255800-80260200	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:80255800-80275400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:80256000-80260200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr6:80256000-80260600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:80256000-80261400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:80256000-80262400	Weak transcription	HSMMtube	muscle
35	chr6:80256000-80263400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr6:80256000-80263800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:80256000-80263800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr6:80256000-80280600	Weak transcription	Adipose Nuclei	Adipose
39	chr6:80256200-80260000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:80256200-80260400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:80256200-80261800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:80256200-80264000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:80256200-80266600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr6:80256400-80259800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:80256400-80259800	Weak transcription	NH-A	brain
46	chr6:80256400-80260000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:80256400-80260000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr6:80256400-80260200	Weak transcription	K562	blood
49	chr6:80256400-80260400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:80256400-80261800	Weak transcription	Stomach Smooth Muscle	stomach

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