Variant report

Variant	rs2284285
Chromosome Location	chr7:107999034-107999035
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107998008..108001072-chr7:108096682..108098603,3	MCF-7	breast:
2	chr7:107996666..108000210-chr7:108094187..108098858,6	MCF-7	breast:
3	chr7:107998919..108001119-chr9:140083490..140085157,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10487846	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs10487849	0.86[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10487851	0.83[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10953562	0.86[CEU][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs10953564	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12056165	0.91[EUR][1000 genomes]
rs12154914	0.91[EUR][1000 genomes]
rs12531089	0.81[JPT][hapmap]
rs12669401	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12669405	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230316	0.81[JPT][hapmap]
rs13244715	0.81[JPT][hapmap]
rs17418660	0.86[CEU][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs17419000	0.86[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs17419221	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs17419906	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267882	0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs2267886	0.82[CEU][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs2284287	0.81[JPT][hapmap]
rs2284288	0.81[JPT][hapmap]
rs2300015	0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs2300016	0.86[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2300017	0.80[EUR][1000 genomes]
rs2300028	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300032	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2300034	0.81[ASN][1000 genomes]
rs4727709	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56056000	0.91[EUR][1000 genomes]
rs60830378	0.91[EUR][1000 genomes]
rs62469223	0.91[EUR][1000 genomes]
rs62469224	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62469225	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66526866	0.90[EUR][1000 genomes]
rs67033131	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs67101551	0.80[EUR][1000 genomes]
rs67652370	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs68029971	0.90[EUR][1000 genomes]
rs6942944	0.91[EUR][1000 genomes]
rs6967405	0.86[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7784390	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs7789982	0.88[EUR][1000 genomes]
rs7804045	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	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
7	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
rs2284285	NRCAM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107988000-108001000	Weak transcription	HSMMtube	muscle
2	chr7:107992600-108007400	Weak transcription	HUVEC	blood vessel
3	chr7:107997800-107999800	Enhancers	Placenta	Placenta
4	chr7:107998200-107999400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:107998200-108000000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:107998200-108000000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:107998200-108000800	Enhancers	HepG2	liver
8	chr7:107998400-107999400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr7:107998600-107999400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:107998600-108000000	Enhancers	Fetal Intestine Large	intestine
11	chr7:107998600-108000200	Enhancers	Fetal Intestine Small	intestine
12	chr7:107998800-107999200	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr7:107998800-107999400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr7:107998800-107999400	Enhancers	Fetal Muscle Leg	muscle
15	chr7:107998800-107999400	Enhancers	NHEK	skin
16	chr7:107998800-107999600	Enhancers	Liver	Liver
17	chr7:107998800-107999600	Enhancers	NH-A	brain
18	chr7:107998800-107999800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr7:107998800-107999800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr7:107998800-108000000	Flanking Active TSS	A549	lung
21	chr7:107998800-108003800	Weak transcription	Pancreas	Pancrea
22	chr7:107999000-107999200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:107999000-107999200	Enhancers	Adipose Nuclei	Adipose
24	chr7:107999000-107999200	Enhancers	Brain Anterior Caudate	brain
25	chr7:107999000-107999400	Enhancers	HMEC	breast
26	chr7:107999000-107999600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr7:107999000-107999600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr7:107999000-107999600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr7:107999000-107999600	Enhancers	Stomach Mucosa	stomach
30	chr7:107999000-107999800	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr7:107999000-107999800	Enhancers	Fetal Kidney	kidney

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