Variant report

Variant	rs2002448
Chromosome Location	chr17:46079756-46079757
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45978418..45980535-chr17:46078748..46080389,2	MCF-7	breast:
2	chr17:46062331..46065308-chr17:46079122..46082112,2	K562	blood:
3	chr17:46024513..46026415-chr17:46079474..46081019,2	K562	blood:
4	chr17:46064874..46067902-chr17:46077258..46079817,3	K562	blood:
5	chr17:46077674..46080583-chr17:46085279..46087507,2	MCF-7	breast:
6	chr17:46068180..46070484-chr17:46078345..46080253,2	K562	blood:
7	chr17:46067363..46070212-chr17:46079475..46083776,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264019	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1076236	0.88[EUR][1000 genomes]
rs2597160	0.87[EUR][1000 genomes]
rs2597175	0.91[EUR][1000 genomes]
rs2905855	0.97[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs757351	0.97[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs886445	0.99[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2002448	SCRN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46068000-46079800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr17:46073400-46081000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:46074200-46079800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr17:46076400-46084600	Enhancers	Fetal Brain Male	brain
5	chr17:46076800-46085600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr17:46077000-46084000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr17:46077400-46079800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr17:46077400-46080400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr17:46077600-46079800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr17:46077600-46079800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr17:46077600-46079800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr17:46077600-46079800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr17:46078400-46079800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr17:46078400-46079800	Enhancers	Fetal Brain Female	brain
15	chr17:46078400-46080200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr17:46078400-46083200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr17:46078600-46079800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:46078600-46083000	Enhancers	HSMMtube	muscle
19	chr17:46078800-46079800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr17:46078800-46079800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr17:46078800-46080400	Enhancers	Brain Germinal Matrix	brain
22	chr17:46078800-46080600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr17:46078800-46081600	Enhancers	Brain Cingulate Gyrus	brain
24	chr17:46078800-46082800	Enhancers	Fetal Stomach	stomach
25	chr17:46078800-46083000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr17:46078800-46084000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:46078800-46084800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr17:46079000-46079800	Enhancers	Colon Smooth Muscle	Colon
29	chr17:46079000-46080400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr17:46079000-46080600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr17:46079000-46080600	Enhancers	Primary B cells from cord blood	blood
32	chr17:46079000-46081800	Enhancers	Adipose Nuclei	Adipose
33	chr17:46079000-46083000	Enhancers	Placenta	Placenta
34	chr17:46079200-46079800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr17:46079200-46081400	Enhancers	Fetal Muscle Trunk	muscle
36	chr17:46079200-46082600	Enhancers	Fetal Muscle Leg	muscle
37	chr17:46079200-46083800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr17:46079200-46083800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr17:46079400-46079800	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr17:46079400-46079800	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr17:46079400-46079800	Enhancers	Brain Anterior Caudate	brain
42	chr17:46079400-46080600	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr17:46079400-46080600	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr17:46079400-46080600	Enhancers	Lung	lung
45	chr17:46079400-46080800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr17:46079400-46082800	Enhancers	H9 Cell Line	embryonic stem cell
47	chr17:46079600-46079800	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr17:46079600-46079800	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr17:46079600-46079800	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr17:46079600-46079800	Enhancers	A549	lung

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