Variant report

Variant	rs4902580
Chromosome Location	chr14:68887568-68887569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:68885394..68888226-chr14:69257512..69260441,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10747299	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158737	1.00[JPT][hapmap]
rs11158742	1.00[JPT][hapmap]
rs12435006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12588330	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12590319	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12897307	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17755674	1.00[JPT][hapmap]
rs1956538	1.00[JPT][hapmap]
rs2064910	1.00[JPT][hapmap]
rs2331703	1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[ASN][1000 genomes]
rs2331704	1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2525507	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2753403	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2842320	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3784118	1.00[JPT][hapmap]
rs3966077	1.00[JPT][hapmap]
rs4899241	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4899243	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4902578	1.00[JPT][hapmap]
rs4902581	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4902582	0.85[ASN][1000 genomes]
rs4902587	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4902588	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4902589	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7145422	1.00[JPT][hapmap]
rs7152152	0.95[GIH][hapmap]
rs7154175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8003606	1.00[CHB][hapmap]
rs8013184	0.81[EUR][1000 genomes]
rs8019592	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9323510	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9743896	0.85[ASN][1000 genomes]
rs975422	1.00[JPT][hapmap]

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	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4902580	MAP3K9	cis	parietal	SCAN
rs4902580	RAB15	cis	parietal	SCAN
rs4902580	HSPA2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68877200-68890600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr14:68881000-68890600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr14:68882200-68890000	Weak transcription	Small Intestine	intestine
4	chr14:68882400-68893400	Weak transcription	Fetal Intestine Small	intestine
5	chr14:68883400-68888200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr14:68884000-68890200	Weak transcription	Primary B cells from cord blood	blood
7	chr14:68884200-68890800	Weak transcription	Colon Smooth Muscle	Colon
8	chr14:68885200-68893600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr14:68885600-68888000	Enhancers	Primary T cells from cord blood	blood
10	chr14:68885800-68889600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr14:68886000-68890600	Weak transcription	Fetal Muscle Leg	muscle
12	chr14:68886200-68888200	Enhancers	Spleen	Spleen
13	chr14:68886200-68894800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr14:68886600-68887600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr14:68886600-68887800	Weak transcription	Ovary	ovary
16	chr14:68886600-68890000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr14:68886600-68903200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr14:68887000-68888400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr14:68887200-68887800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr14:68887200-68887800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr14:68887200-68887800	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr14:68887200-68888000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr14:68887200-68888000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr14:68887200-68888000	Enhancers	Fetal Kidney	kidney
25	chr14:68887200-68888000	Enhancers	Fetal Lung	lung
26	chr14:68887200-68888200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr14:68887200-68888200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr14:68887200-68888200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr14:68887200-68888400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr14:68887400-68888000	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr14:68887400-68888000	Enhancers	Fetal Heart	heart
32	chr14:68887400-68888000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr14:68887400-68888200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr14:68887400-68888200	Enhancers	K562	blood

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