Variant report

Variant	rs2267882
Chromosome Location	chr7:107948721-107948722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107948237..107951019-chr7:107962577..107964592,2	MCF-7	breast:
2	chr7:107941830..107944021-chr7:107948605..107950880,3	MCF-7	breast:
3	chr7:107832494..107835185-chr7:107947670..107949448,2	MCF-7	breast:
4	chr7:107944268..107947036-chr7:107947999..107949579,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10487846	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10487849	1.00[ASW][hapmap];0.91[CEU][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10487851	0.86[CEU][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10953562	1.00[ASW][hapmap];0.91[CEU][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10953564	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12056165	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12154914	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12669401	0.81[EUR][1000 genomes]
rs12669405	0.82[EUR][1000 genomes]
rs17418660	1.00[ASW][hapmap];0.91[CEU][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17419000	1.00[ASW][hapmap];0.91[CEU][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17419221	0.91[CEU][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17419906	0.84[ASW][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap]
rs2267886	0.85[CEU][hapmap];0.85[JPT][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2284285	0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs2300015	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2300016	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2300017	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2300028	0.82[CEU][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs2300032	0.82[EUR][1000 genomes]
rs2300033	0.84[ASW][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap]
rs56056000	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60830378	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62469223	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62469224	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62469225	0.80[EUR][1000 genomes]
rs66526866	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67033131	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67101551	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67652370	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs68029971	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6942944	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6967405	0.91[CEU][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7784390	0.90[CEU][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7789982	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS 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	91 gene(s)	inside rSNPs	diseases
2	nsv949344	chr7:107396502-107987085	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1030425	chr7:107910716-108041036	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1019059	chr7:107935905-107995523	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv1021783	chr7:107935905-107998281	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	esv2761354	chr7:107935905-107998293	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv1031824	chr7:107935905-108006038	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	nsv1017288	chr7:107939739-108000837	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2267882	LHFPL3	cis	parietal	SCAN
rs2267882	NRCAM	cis	lymphoblastoid	seeQTL
rs2267882	LHFPL3	cis	cerebellum	SCAN
rs2267882	NRCAM	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107925400-107952000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:107932000-107950600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:107935400-107950600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr7:107940400-107964400	Weak transcription	Pancreas	Pancrea
5	chr7:107945400-107953800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:107945600-107954000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr7:107945800-107952600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:107945800-107954000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:107945800-107956000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:107947000-107949000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:107947000-107949400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:107947000-107953800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:107947200-107948800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:107947200-107951400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:107947400-107951000	Enhancers	Brain Cingulate Gyrus	brain
16	chr7:107947600-107949000	Enhancers	HSMM	muscle
17	chr7:107947600-107949200	Enhancers	NHEK	skin
18	chr7:107947600-107949400	Enhancers	Placenta Amnion	Placenta Amnion
19	chr7:107947600-107949800	Enhancers	Brain Substantia Nigra	brain
20	chr7:107947600-107950200	Enhancers	A549	lung
21	chr7:107947600-107950800	Enhancers	Brain Anterior Caudate	brain
22	chr7:107947600-107951600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr7:107947600-107952600	Enhancers	HSMMtube	muscle
24	chr7:107947600-107953400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:107947600-107953800	Enhancers	HMEC	breast
26	chr7:107947600-107954000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:107947600-107955200	Enhancers	HUVEC	blood vessel
28	chr7:107947800-107949000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr7:107947800-107949400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:107947800-107953400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr7:107948000-107949200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr7:107948000-107951600	Weak transcription	Brain Hippocampus Middle	brain
33	chr7:107948000-107952000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr7:107948000-107965200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr7:107948200-107949400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:107948200-107951400	Enhancers	GM12878-XiMat	blood
37	chr7:107948200-107953800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr7:107948400-107949000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr7:107948400-107949400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr7:107948400-107949400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr7:107948400-107949600	Enhancers	Adipose Nuclei	Adipose
42	chr7:107948400-107950000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr7:107948400-107950000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr7:107948400-107950600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr7:107948400-107950800	Weak transcription	Esophagus	oesophagus
46	chr7:107948600-107949400	Enhancers	NHDF-Ad	bronchial
47	chr7:107948600-107949600	Enhancers	Brain Angular Gyrus	brain
48	chr7:107948600-107949600	Enhancers	NH-A	brain
49	chr7:107948600-107950000	Enhancers	Osteobl	bone
50	chr7:107948600-107952600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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