Variant report

Variant	rs6660484
Chromosome Location	chr1:92172608-92172609
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:92170602..92173339-chr1:92193646..92196655,3	K562	blood:
2	chr1:92172545..92174973-chr1:92176760..92181587,6	K562	blood:
3	chr1:92169004..92174919-chr1:92176719..92181810,13	K562	blood:
4	chr1:92147184..92150173-chr1:92170826..92172983,2	K562	blood:
5	chr1:92171556..92174319-chr1:92192044..92194001,2	K562	blood:
6	chr1:92166691..92169573-chr1:92171812..92173535,2	K562	blood:
7	chr1:92171317..92173686-chr1:92182060..92185039,2	K562	blood:
8	chr1:92162419..92165412-chr1:92170320..92173271,4	K562	blood:
9	chr1:92171820..92173594-chr1:92174594..92176348,2	K562	blood:
10	chr1:92162419..92166265-chr1:92170255..92173059,5	K562	blood:
11	chr1:92057409..92061312-chr1:92170673..92173610,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000069702	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10783003	0.81[GIH][hapmap]
rs11165293	0.83[CHB][hapmap]
rs11165294	0.83[CHB][hapmap]
rs11165354	0.81[GIH][hapmap]
rs2038931	0.83[CHB][hapmap]
rs2391027	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs284874	0.89[CEU][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3767576	0.82[CHB][hapmap]
rs4370805	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4650271	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7514724	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv2763581	chr1:92068967-92203803	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1014990	chr1:92084142-92206674	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers 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	33 gene(s)	inside rSNPs	diseases
7	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6660484	LRRC8B	cis	parietal	SCAN
rs6660484	ALG14	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92149400-92172800	Weak transcription	Esophagus	oesophagus
2	chr1:92151200-92172800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:92152600-92184200	Strong transcription	HepG2	liver
4	chr1:92153000-92197000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:92155400-92178800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:92155600-92178800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:92155800-92191200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:92156000-92172800	Weak transcription	Gastric	stomach
9	chr1:92156200-92172800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:92156200-92177800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:92159000-92173600	Weak transcription	Fetal Kidney	kidney
12	chr1:92159400-92172800	Weak transcription	Aorta	Aorta
13	chr1:92159400-92173400	Weak transcription	Brain Substantia Nigra	brain
14	chr1:92159800-92172800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:92159800-92172800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:92159800-92183800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:92163200-92172800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:92163200-92172800	Weak transcription	Spleen	Spleen
19	chr1:92163200-92176800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:92163800-92173400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:92164000-92172800	Weak transcription	Fetal Intestine Small	intestine
22	chr1:92164000-92184400	Weak transcription	Hela-S3	cervix
23	chr1:92164000-92195000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:92164200-92173200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:92164200-92175000	Weak transcription	GM12878-XiMat	blood
26	chr1:92164200-92176000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr1:92164800-92177800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:92165000-92172800	Weak transcription	Right Ventricle	heart
29	chr1:92165200-92177400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:92165400-92178600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:92165400-92178600	Weak transcription	Fetal Brain Male	brain
32	chr1:92165600-92175400	Strong transcription	Stomach Smooth Muscle	stomach
33	chr1:92165800-92172800	Weak transcription	Fetal Lung	lung
34	chr1:92165800-92184800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:92165800-92196800	Weak transcription	Small Intestine	intestine
36	chr1:92166000-92172800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:92166200-92172800	Weak transcription	Right Atrium	heart
38	chr1:92166200-92173000	Weak transcription	HSMMtube	muscle
39	chr1:92166400-92173000	Strong transcription	Placenta	Placenta
40	chr1:92166600-92191000	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:92167400-92184800	Weak transcription	A549	lung
42	chr1:92167800-92172800	Weak transcription	Pancreas	Pancrea
43	chr1:92167800-92172800	Weak transcription	NHLF	lung
44	chr1:92167800-92178000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:92167800-92178200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:92168000-92178600	Weak transcription	Osteobl	bone
47	chr1:92168000-92191000	Weak transcription	HUVEC	blood vessel
48	chr1:92168800-92173000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr1:92169200-92178800	Strong transcription	Liver	Liver
50	chr1:92169400-92172800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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