Variant report

Variant	rs12667471
Chromosome Location	chr7:140076938-140076939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:140075069..140077735-chr7:140096588..140099526,2	MCF-7	breast:
2	chr7:140075072..140077306-chr7:140082163..140084967,2	K562	blood:

Variant related genes	Relation type
ENSG00000157800	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10251020	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs11763598	0.91[CHB][hapmap];0.83[CHD][hapmap];0.89[MKK][hapmap]
rs12669654	0.83[ASW][hapmap];0.83[CHB][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap]
rs12673021	0.81[AMR][1000 genomes]
rs12703771	0.96[MEX][hapmap]
rs12703792	0.96[MEX][hapmap]
rs12703793	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12703796	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12703797	0.80[EUR][1000 genomes]
rs12703799	0.88[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3924962	1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs4341086	0.81[CEU][hapmap]
rs4368896	0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4448174	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4726780	0.80[EUR][1000 genomes]
rs62490396	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62490397	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62490398	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6464713	0.82[AFR][1000 genomes]
rs6953541	0.83[ASW][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap]
rs6953981	0.96[MEX][hapmap]
rs6970664	0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6976805	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7777207	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7786963	0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7792038	0.96[MEX][hapmap]
rs7796411	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7803606	0.81[AFR][1000 genomes]
rs9692001	0.81[AMR][1000 genomes];0.81[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12667471	CREB3L2	cis	parietal	SCAN
rs12667471	TRIM2	trans	cerebellum	SCAN
rs12667471	OR9A2	cis	cerebellum	SCAN
rs12667471	ZC3HAV1L	cis	parietal	SCAN
rs12667471	MGAM	cis	parietal	SCAN
rs12667471	SLC37A3	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 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	chr7:140042000-140084800	Weak transcription	Hela-S3	cervix
4	chr7:140047600-140084200	Weak transcription	Fetal Brain Male	brain
5	chr7:140049200-140090200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:140049600-140078000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:140049600-140078600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:140049600-140079400	Weak transcription	Brain Substantia Nigra	brain
9	chr7:140050200-140079200	Weak transcription	HUVEC	blood vessel
10	chr7:140052000-140097400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr7:140052800-140079600	Weak transcription	NHDF-Ad	bronchial
12	chr7:140054200-140079800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:140054600-140077800	Weak transcription	Brain Angular Gyrus	brain
14	chr7:140055000-140077800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr7:140055600-140079200	Weak transcription	Fetal Kidney	kidney
16	chr7:140056800-140077400	Weak transcription	NH-A	brain
17	chr7:140056800-140079400	Weak transcription	Colonic Mucosa	Colon
18	chr7:140058600-140077800	Weak transcription	Brain Hippocampus Middle	brain
19	chr7:140058600-140096000	Weak transcription	Small Intestine	intestine
20	chr7:140058800-140077800	Weak transcription	Placenta	Placenta
21	chr7:140058800-140079200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr7:140058800-140081400	Weak transcription	A549	lung
23	chr7:140058800-140084400	Weak transcription	Gastric	stomach
24	chr7:140058800-140097200	Weak transcription	Brain Anterior Caudate	brain
25	chr7:140059400-140091400	Weak transcription	Fetal Heart	heart
26	chr7:140063400-140082600	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr7:140065000-140077000	Weak transcription	HMEC	breast
28	chr7:140065000-140077800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr7:140065200-140079200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr7:140066600-140077800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:140067800-140077800	Weak transcription	HSMMtube	muscle
32	chr7:140068000-140089000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr7:140068400-140078800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr7:140069000-140077400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr7:140069000-140077800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr7:140069000-140077800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr7:140069000-140078400	Weak transcription	Spleen	Spleen
38	chr7:140069200-140077800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr7:140069200-140077800	Weak transcription	Left Ventricle	heart
40	chr7:140069200-140082000	Weak transcription	Colon Smooth Muscle	Colon
41	chr7:140069400-140077800	Weak transcription	Ovary	ovary
42	chr7:140069400-140079200	Weak transcription	Brain Germinal Matrix	brain
43	chr7:140069600-140091800	Weak transcription	Esophagus	oesophagus
44	chr7:140070400-140077800	Weak transcription	HSMM	muscle
45	chr7:140072000-140082400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:140072400-140079600	Weak transcription	NHEK	skin
47	chr7:140074000-140082200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr7:140074000-140082200	Strong transcription	Fetal Stomach	stomach
49	chr7:140074200-140082400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:140074600-140078600	Weak transcription	Lung	lung

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