Variant report

Variant	rs16890846
Chromosome Location	chr6:80263048-80263049
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:79786657..79788445-chr6:80262808..80265687,2	K562	blood:

Variant related genes	Relation type
ENSG00000146247	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];0.85[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];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11756302	0.97[AMR][1000 genomes];0.98[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];0.89[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];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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890791	0.85[CHD][hapmap]
rs16890821	0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs16890842	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];0.99[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];0.86[EUR][1000 genomes]
rs2069304	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2455943	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455944	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655665	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2655686	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655689	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655693	0.81[CEU][hapmap]
rs2803172	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803176	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803177	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803178	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803179	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2803180	0.83[ASN][1000 genomes]
rs2812697	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2812699	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34068461	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[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];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55951062	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56311322	0.93[AMR][1000 genomes];0.99[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];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72901839	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7743617	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7755562	0.85[JPT][hapmap]
rs7771276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774418	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.86[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];0.98[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];0.86[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
rs16890846	LCA5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80247600-80267800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:80248800-80272000	Weak transcription	Ovary	ovary
3	chr6:80254400-80267800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:80254400-80271400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:80254400-80273000	Weak transcription	Left Ventricle	heart
6	chr6:80254600-80273800	Weak transcription	Stomach Mucosa	stomach
7	chr6:80255000-80280000	Weak transcription	Aorta	Aorta
8	chr6:80255200-80264800	Weak transcription	Fetal Heart	heart
9	chr6:80255200-80267800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:80255600-80264800	Weak transcription	Fetal Intestine Large	intestine
11	chr6:80255600-80279400	Weak transcription	HMEC	breast
12	chr6:80255600-80280000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:80255800-80275400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:80256000-80263400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:80256000-80263800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:80256000-80263800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr6:80256000-80280600	Weak transcription	Adipose Nuclei	Adipose
18	chr6:80256200-80264000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:80256200-80266600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:80256400-80263800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:80256400-80263800	Weak transcription	Brain Angular Gyrus	brain
22	chr6:80256400-80264000	Weak transcription	Brain Substantia Nigra	brain
23	chr6:80256400-80264200	Weak transcription	Osteobl	bone
24	chr6:80256400-80267200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:80256400-80267600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:80257200-80268600	Weak transcription	Spleen	Spleen
27	chr6:80257400-80263400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:80257400-80268000	Weak transcription	Fetal Stomach	stomach
29	chr6:80257400-80273200	Weak transcription	Pancreas	Pancrea
30	chr6:80257400-80278600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:80257400-80278600	Weak transcription	Fetal Kidney	kidney
32	chr6:80257600-80274200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:80257800-80277800	Weak transcription	Fetal Intestine Small	intestine
34	chr6:80258600-80279200	Weak transcription	Fetal Lung	lung
35	chr6:80260000-80263200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:80260600-80272800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:80260600-80274400	Weak transcription	Fetal Brain Female	brain
38	chr6:80260600-80278600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:80260800-80264200	Weak transcription	NH-A	brain
40	chr6:80260800-80275400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:80260800-80280200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr6:80260800-80280200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr6:80260800-80280400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr6:80260800-80283000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:80261400-80271600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:80261600-80263400	Enhancers	HepG2	liver
47	chr6:80261800-80280200	Weak transcription	Fetal Muscle Leg	muscle
48	chr6:80262600-80263200	Enhancers	Brain Anterior Caudate	brain
49	chr6:80262600-80263200	Strong transcription	HSMM	muscle
50	chr6:80263000-80263200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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