Variant report

Variant	rs2300015
Chromosome Location	chr7:107943886-107943887
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107935963..107938050-chr7:107942181..107944015,2	K562	blood:
2	chr7:107943761..107946281-chr7:107950913..107952472,2	MCF-7	breast:
3	chr7:107942489..107944255-chr7:107991552..107993879,2	MCF-7	breast:
4	chr7:107942852..107945824-chr7:108094045..108096766,3	MCF-7	breast:
5	chr7:107942231..107944155-chr7:107945358..107947357,2	MCF-7	breast:
6	chr7:107941830..107944021-chr7:107948605..107950880,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10487846	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10487849	0.91[CEU][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10487851	0.86[CEU][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10953562	0.91[CEU][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10953564	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12056165	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12154914	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12669405	0.80[EUR][1000 genomes]
rs17418660	0.91[CEU][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17419000	0.91[CEU][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17419221	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17419906	0.82[YRI][hapmap]
rs2267882	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]
rs2267886	0.85[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2284285	0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs2300016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2300017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300028	0.83[CEU][hapmap];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs2300032	0.80[EUR][1000 genomes]
rs2300033	0.82[YRI][hapmap]
rs56056000	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60830378	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62469223	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62469224	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66526866	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67033131	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67101551	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67652370	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs68029971	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6942944	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6967405	0.91[CEU][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7784390	0.90[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7789982	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2300015	NRCAM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 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	chr7:107931000-107947400	Weak transcription	Fetal Brain Female	brain
3	chr7:107932000-107950600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:107933600-107947400	Weak transcription	Brain Hippocampus Middle	brain
5	chr7:107935200-107947000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:107935400-107950600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:107936600-107946800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:107940200-107947400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr7:107940400-107947600	Weak transcription	Brain Substantia Nigra	brain
10	chr7:107940400-107964400	Weak transcription	Pancreas	Pancrea
11	chr7:107940600-107945400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:107940600-107945600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr7:107940600-107945800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:107940600-107945800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:107940600-107945800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr7:107942800-107947200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr7:107943000-107947600	Weak transcription	Brain Angular Gyrus	brain
18	chr7:107943000-107948400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:107943200-107945800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:107943200-107945800	Weak transcription	A549	lung
21	chr7:107943200-107947600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr7:107943200-107948200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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