Variant report

Variant	rs12669654
Chromosome Location	chr7:140066411-140066412
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140063593..140066561-chr7:140103123..140105495,2	MCF-7	breast:
2	chr7:140066075..140068956-chr7:140069820..140072197,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MKRN1-7	chr7:140065607-140068356	ucscGeneNc_uc003vwb_1

Variant related genes	Relation type
ENSG00000223113	Chromatin interaction
ENSG00000157800	Chromatin interaction
ENSG00000146955	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10235190	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11763598	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12667471	0.83[ASW][hapmap];0.83[CHB][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap]
rs12703793	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12703794	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12703796	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12703799	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4341086	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4368896	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4448174	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4587251	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62490397	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62490398	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6464710	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6464713	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6953541	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6970664	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6976805	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7786963	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7796411	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7803606	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022919	chr7:140043299-140120546	Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2762706	chr7:140054170-140119629	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv522190	chr7:140066411-140130663	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12669654	NDUFB2	cis	cerebellum	SCAN
rs12669654	SLC37A3	cis	multi-tissue	Pritchard
rs12669654	OR9A2	cis	cerebellum	SCAN
rs12669654	ZC3HAV1L	cis	parietal	SCAN
rs12669654	TRIM2	trans	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140033600-140096000	Weak transcription	Stomach Mucosa	stomach
2	chr7:140034800-140085600	Weak transcription	Psoas Muscle	Psoas
3	chr7:140035000-140074200	Weak transcription	Right Atrium	heart
4	chr7:140042000-140084800	Weak transcription	Hela-S3	cervix
5	chr7:140046000-140076200	Weak transcription	Right Ventricle	heart
6	chr7:140047600-140084200	Weak transcription	Fetal Brain Male	brain
7	chr7:140049200-140090200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:140049600-140067800	Weak transcription	Colon Smooth Muscle	Colon
9	chr7:140049600-140076000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:140049600-140078000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr7:140049600-140078600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:140049600-140079400	Weak transcription	Brain Substantia Nigra	brain
13	chr7:140050200-140079200	Weak transcription	HUVEC	blood vessel
14	chr7:140051400-140068400	Weak transcription	HSMM	muscle
15	chr7:140051600-140076400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr7:140052000-140097400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr7:140052600-140075600	Weak transcription	Pancreas	Pancrea
18	chr7:140052800-140079600	Weak transcription	NHDF-Ad	bronchial
19	chr7:140054200-140079800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr7:140054600-140077800	Weak transcription	Brain Angular Gyrus	brain
21	chr7:140055000-140068600	Weak transcription	Primary B cells from cord blood	blood
22	chr7:140055000-140068600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr7:140055000-140077800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr7:140055600-140067400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr7:140055600-140079200	Weak transcription	Fetal Kidney	kidney
26	chr7:140056800-140077400	Weak transcription	NH-A	brain
27	chr7:140056800-140079400	Weak transcription	Colonic Mucosa	Colon
28	chr7:140057200-140067400	Weak transcription	HSMMtube	muscle
29	chr7:140057400-140075400	Weak transcription	Osteobl	bone
30	chr7:140058400-140067400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr7:140058600-140075400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr7:140058600-140075600	Weak transcription	HepG2	liver
33	chr7:140058600-140077800	Weak transcription	Brain Hippocampus Middle	brain
34	chr7:140058600-140096000	Weak transcription	Small Intestine	intestine
35	chr7:140058800-140067400	Weak transcription	Adipose Nuclei	Adipose
36	chr7:140058800-140067400	Weak transcription	Left Ventricle	heart
37	chr7:140058800-140067800	Weak transcription	Esophagus	oesophagus
38	chr7:140058800-140075600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr7:140058800-140075600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr7:140058800-140075600	Weak transcription	Aorta	Aorta
41	chr7:140058800-140077800	Weak transcription	Placenta	Placenta
42	chr7:140058800-140079200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr7:140058800-140081400	Weak transcription	A549	lung
44	chr7:140058800-140084400	Weak transcription	Gastric	stomach
45	chr7:140058800-140097200	Weak transcription	Brain Anterior Caudate	brain
46	chr7:140059000-140067400	Weak transcription	Ovary	ovary
47	chr7:140059400-140067000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr7:140059400-140067000	Weak transcription	Thymus	Thymus
49	chr7:140059400-140067400	Weak transcription	Lung	lung
50	chr7:140059400-140067800	Weak transcription	Spleen	Spleen

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