Variant report

Variant	rs1990162
Chromosome Location	chr7:108055235-108055236
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:108054248..108057900-chr7:108068091..108071582,3	MCF-7	breast:
2	chr7:108006500..108008005-chr7:108054331..108056945,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10230518	0.81[ASN][1000 genomes]
rs11983030	0.92[CEU][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12333431	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2108256	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2284290	0.80[CEU][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2300037	0.92[CEU][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2300043	0.92[CEU][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2300049	0.87[CEU][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2300050	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4141076	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4730307	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4730309	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4730320	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs61550883	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[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	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	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
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1990162	NRCAM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108049400-108056400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:108050000-108056400	Weak transcription	Fetal Brain Female	brain
3	chr7:108053800-108056400	Enhancers	Muscle Satellite Cultured Cells	--
4	chr7:108054000-108056400	Enhancers	HSMMtube	muscle
5	chr7:108054200-108055400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr7:108054200-108055400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:108054200-108055400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:108054200-108055400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr7:108054200-108055400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:108054200-108055600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr7:108054200-108055600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr7:108054200-108055600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:108054200-108055800	Enhancers	HMEC	breast
14	chr7:108054200-108056000	Enhancers	Primary hematopoietic stem cells	blood
15	chr7:108054200-108056200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr7:108054200-108056400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:108054200-108056400	Enhancers	Primary B cells from peripheral blood	blood
18	chr7:108054200-108056600	Enhancers	Brain Angular Gyrus	brain
19	chr7:108054200-108056800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:108054200-108057000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:108054200-108057000	Enhancers	Fetal Muscle Leg	muscle
22	chr7:108054200-108057600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:108054200-108057600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:108054200-108057600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr7:108054200-108057600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr7:108054200-108057800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr7:108054200-108058600	Enhancers	Brain Anterior Caudate	brain
28	chr7:108054200-108058800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr7:108054200-108059200	Enhancers	HUVEC	blood vessel
30	chr7:108054400-108055400	Enhancers	Brain Hippocampus Middle	brain
31	chr7:108054400-108055400	Flanking Active TSS	A549	lung
32	chr7:108054400-108055800	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr7:108054400-108055800	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr7:108054400-108056400	Enhancers	GM12878-XiMat	blood
35	chr7:108054400-108056600	Enhancers	Primary B cells from cord blood	blood
36	chr7:108054600-108056200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr7:108054600-108056400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr7:108054600-108056400	Enhancers	HSMM	muscle
39	chr7:108054600-108056600	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr7:108054600-108056600	Weak transcription	NHDF-Ad	bronchial
41	chr7:108054600-108057600	Enhancers	Brain Cingulate Gyrus	brain
42	chr7:108054800-108056200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr7:108054800-108056400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:108054800-108056600	Weak transcription	Osteobl	bone
45	chr7:108054800-108061000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr7:108055000-108055400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr7:108055000-108055400	Enhancers	Brain Substantia Nigra	brain
48	chr7:108055000-108055600	Enhancers	Brain Germinal Matrix	brain
49	chr7:108055000-108055800	Enhancers	Pancreas	Pancrea
50	chr7:108055000-108056400	Weak transcription	NH-A	brain

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