Variant report

Variant	rs2246113
Chromosome Location	chr6:88410050-88410051
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:88406148..88410116-chr6:88433158..88435018,3	K562	blood:
2	chr6:88408898..88411861-chr6:88430189..88432233,3	K562	blood:
3	chr6:88409661..88412134-chr6:88428970..88430720,2	MCF-7	breast:
4	chr6:88408810..88411084-chr6:88834084..88837028,2	K562	blood:
5	chr6:88180469..88184304-chr6:88409511..88413377,7	K562	blood:
6	chr6:88116486..88118287-chr6:88408071..88410936,2	MCF-7	breast:
7	chr6:88372101..88374579-chr6:88409088..88410722,2	K562	blood:
8	chr6:88307562..88310248-chr6:88408505..88411204,2	K562	blood:
9	chr6:88409009..88410589-chr6:88542039..88544851,2	K562	blood:
10	chr6:88180469..88184304-chr6:88409409..88413377,5	K562	blood:
11	chr6:88298942..88303064-chr6:88409165..88412231,4	K562	blood:
12	chr6:88301564..88305247-chr6:88408310..88410665,3	K562	blood:
13	chr6:88391827..88396132-chr6:88405533..88410317,6	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RARS2-4	chr6:88410020-88410933	NONHSAT113914

No data

Variant related genes	Relation type
ENSG00000135336	Chromatin interaction
ENSG00000164414	Chromatin interaction
ENSG00000238628	Chromatin interaction
ENSG00000272514	Chromatin interaction
ENSG00000213204	Chromatin interaction
ENSG00000146282	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1051131	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs1051148	0.92[CEU][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap]
rs10755484	0.92[CEU][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap]
rs13193380	0.83[EUR][1000 genomes]
rs13194003	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2300909	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs2307379	0.89[EUR][1000 genomes]
rs2754245	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap]
rs2754247	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2754248	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2754260	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2754262	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2754264	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2787893	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2787921	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2787924	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2787927	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[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]
rs2787930	0.82[EUR][1000 genomes]
rs2787934	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2814712	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3757368	0.96[CEU][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap]
rs3934838	0.96[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs4334949	0.96[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs4464759	0.92[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs4498321	0.86[EUR][1000 genomes]
rs4587138	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4587143	0.96[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs4706294	0.87[EUR][1000 genomes]
rs4707374	0.81[EUR][1000 genomes]
rs4707376	0.83[EUR][1000 genomes]
rs4707377	0.83[EUR][1000 genomes]
rs4707379	0.83[EUR][1000 genomes]
rs4707382	0.87[EUR][1000 genomes]
rs4707383	0.87[EUR][1000 genomes]
rs6454631	0.85[JPT][hapmap]
rs6454636	0.87[EUR][1000 genomes]
rs6454638	0.87[EUR][1000 genomes]
rs6454640	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6454641	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6908386	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6916732	0.96[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs6928160	0.81[EUR][1000 genomes]
rs6930600	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6931069	0.88[EUR][1000 genomes]
rs6940150	0.83[EUR][1000 genomes]
rs7741825	0.82[JPT][hapmap]
rs7742965	0.83[EUR][1000 genomes]
rs7746465	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7750207	0.83[EUR][1000 genomes]
rs7755167	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7757636	0.82[EUR][1000 genomes]
rs7757794	0.81[EUR][1000 genomes]
rs7772561	0.87[EUR][1000 genomes]
rs7773906	0.96[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs9444519	0.96[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs9444522	0.87[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs9444524	0.83[EUR][1000 genomes]
rs9444525	0.86[EUR][1000 genomes]
rs9444526	0.86[EUR][1000 genomes]
rs9450723	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs9450732	0.96[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs9450733	0.80[EUR][1000 genomes]
rs9450738	0.83[EUR][1000 genomes]
rs9450739	0.83[EUR][1000 genomes]
rs9450744	0.83[EUR][1000 genomes]
rs9450752	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs9450755	0.83[EUR][1000 genomes]
rs9450762	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs985764	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv7941	chr6:88403555-88413595	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2246113	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs2246113	SLC35A1	cis	multi-tissue	Pritchard
rs2246113	GJB7	cis	cerebellum	SCAN
rs2246113	SNORD50A	cis	cerebellum	SCAN
rs2246113	C6orf162	cis	parietal	SCAN
rs2246113	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs2246113	C6orf162	cis	cerebellum	SCAN
rs2246113	C6orf164	cis	Thyroid	GTEx
rs2246113	SLC35A1	cis	lymphoblastoid	seeQTL
rs2246113	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs2246113	SLC35A1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88388000-88410400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:88406000-88410200	Weak transcription	Gastric	stomach
3	chr6:88407000-88410200	Active TSS	Fetal Brain Female	brain
4	chr6:88407000-88410400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:88407000-88410400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:88407000-88412800	Active TSS	Thymus	Thymus
7	chr6:88407200-88410600	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr6:88407200-88410800	Active TSS	Right Atrium	heart
9	chr6:88407200-88411000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:88407400-88410400	Active TSS	Brain Germinal Matrix	brain
11	chr6:88407400-88411000	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr6:88407400-88411200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:88407400-88412600	Active TSS	Colonic Mucosa	Colon
14	chr6:88407400-88412600	Active TSS	Ovary	ovary
15	chr6:88407400-88412800	Active TSS	Aorta	Aorta
16	chr6:88407400-88413200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:88407400-88413200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:88407400-88413200	Active TSS	Psoas Muscle	Psoas
19	chr6:88407600-88412800	Active TSS	H1 Cell Line	embryonic stem cell
20	chr6:88407600-88413000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr6:88407600-88413000	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr6:88407600-88413000	Active TSS	HSMMtube	muscle
23	chr6:88407800-88412800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:88408000-88410200	Weak transcription	Pancreas	Pancrea
25	chr6:88408000-88410600	Weak transcription	Spleen	Spleen
26	chr6:88408000-88411000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:88408000-88412200	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr6:88408000-88412600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:88408000-88412600	Active TSS	A549	lung
30	chr6:88408000-88412800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:88408000-88412800	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr6:88408000-88412800	Active TSS	Fetal Intestine Large	intestine
33	chr6:88408000-88412800	Active TSS	Fetal Intestine Small	intestine
34	chr6:88408000-88412800	Active TSS	Fetal Muscle Leg	muscle
35	chr6:88408000-88413000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:88408000-88413000	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr6:88408000-88413000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:88408000-88413000	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr6:88408000-88413000	Active TSS	Stomach Smooth Muscle	stomach
40	chr6:88408000-88413000	Active TSS	HMEC	breast
41	chr6:88408000-88413000	Active TSS	HSMM	muscle
42	chr6:88408000-88413000	Active TSS	NHDF-Ad	bronchial
43	chr6:88408000-88413200	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr6:88408200-88412200	Active TSS	Hela-S3	cervix
45	chr6:88408200-88412200	Active TSS	Osteobl	bone
46	chr6:88408200-88412400	Active TSS	Primary monocytes fromperipheralblood	blood
47	chr6:88408200-88412600	Active TSS	Primary T cells fromperipheralblood	blood
48	chr6:88408200-88412800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr6:88408200-88412800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr6:88408200-88412800	Active TSS	Placenta	Placenta

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