Variant report

Variant	rs2715630
Chromosome Location	chr3:133599961-133599962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:133591457..133594104-chr3:133599592..133601842,2	MCF-7	breast:
2	chr3:133595806..133598075-chr3:133598374..133600907,3	K562	blood:
3	chr3:133599032..133602224-chr3:133604113..133606875,3	MCF-7	breast:
4	chr3:133599732..133601773-chr3:133618938..133620509,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1106735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1525885	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1525887	0.87[ASN][1000 genomes]
rs1525888	0.87[ASN][1000 genomes]
rs1917779	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1917781	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs1949882	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap]
rs2030821	0.87[ASN][1000 genomes]
rs2140920	0.87[ASN][1000 genomes]
rs2692679	0.87[ASN][1000 genomes]
rs2692680	0.81[AFR][1000 genomes]
rs2692682	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2692687	0.87[ASN][1000 genomes]
rs2692689	0.87[ASN][1000 genomes]
rs2692693	0.87[ASN][1000 genomes]
rs2715612	0.87[ASN][1000 genomes]
rs2715617	0.87[ASN][1000 genomes]
rs2715619	0.99[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2715620	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2715635	0.88[CHB][hapmap]
rs57405758	0.98[ASN][1000 genomes]
rs7641134	0.88[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	nsv933605	chr3:133425907-133680641	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv829729	chr3:133444871-133620387	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2715630	NCK1	cis	parietal	SCAN
rs2715630	EPHB1	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133590600-133606600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:133592000-133602000	Weak transcription	Brain Angular Gyrus	brain
3	chr3:133592400-133602800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:133592400-133605800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:133596200-133600000	Weak transcription	K562	blood
6	chr3:133596400-133613600	Weak transcription	Gastric	stomach
7	chr3:133598200-133601400	ZNF genes & repeats	Brain Germinal Matrix	brain
8	chr3:133598400-133600400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr3:133598600-133600000	Weak transcription	Fetal Brain Female	brain
10	chr3:133598600-133602800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:133598800-133610400	Weak transcription	Fetal Brain Male	brain
12	chr3:133599000-133600800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:133599000-133602200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:133599000-133602200	Enhancers	GM12878-XiMat	blood
15	chr3:133599200-133600400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:133599400-133600000	Enhancers	Fetal Muscle Trunk	muscle
17	chr3:133599400-133602600	Weak transcription	Left Ventricle	heart
18	chr3:133599400-133602800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr3:133599600-133601800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:133599600-133610600	Weak transcription	Pancreas	Pancrea
21	chr3:133599800-133601000	Weak transcription	Brain Anterior Caudate	brain
22	chr3:133599800-133601200	Weak transcription	Brain Substantia Nigra	brain
23	chr3:133599800-133601600	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:133599800-133603000	Weak transcription	Spleen	Spleen
25	chr3:133599800-133606200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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