Variant report

Variant	rs10009384
Chromosome Location	chr4:78114283-78114284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78077628..78079889-chr4:78114181..78117091,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138764	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10005142	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10010290	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10017014	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10018359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10020351	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10025838	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs10026129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10026646	0.89[TSI][hapmap]
rs10026795	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10030727	0.83[EUR][1000 genomes]
rs10030735	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs10030867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1006042	0.87[JPT][hapmap]
rs10856957	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097728	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11097729	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11097741	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12500115	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs12504397	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12508219	0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12509168	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs12640093	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs1477314	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1559119	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.82[ASN][1000 genomes]
rs1559122	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17397604	0.83[EUR][1000 genomes]
rs1968235	0.82[ASN][1000 genomes]
rs2042228	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs28503908	0.85[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4150106	0.89[TSI][hapmap]
rs4280759	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4285107	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4504280	0.81[ASN][1000 genomes]
rs4536958	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4538513	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4547817	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4563522	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs4576030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4582179	0.83[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4582180	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859475	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859477	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859751	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4859752	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4859753	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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859756	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs4859758	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55663411	0.83[EUR][1000 genomes]
rs6532904	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6532919	0.82[ASN][1000 genomes]
rs6532921	0.92[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6822794	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.82[ASN][1000 genomes]
rs6838744	0.82[ASN][1000 genomes]
rs6840915	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs6844009	0.82[ASN][1000 genomes]
rs6845599	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap]
rs6846698	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6857792	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs7690427	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	nsv879500	chr4:78045960-78115334	Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1000730	chr4:78109138-78210296	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10009384	CXCL13	cis	cerebellum	SCAN
rs10009384	MTHFD2L	cis	parietal	SCAN
rs10009384	CCNG2	cis	cerebellum	SCAN
rs10009384	FRAS1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78109000-78114400	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:78112000-78114800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:78112000-78116200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:78112000-78117400	Weak transcription	Fetal Muscle Leg	muscle
5	chr4:78112000-78120600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:78112200-78120600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:78113600-78118600	Weak transcription	NHEK	skin
8	chr4:78113600-78120400	Weak transcription	HMEC	breast
9	chr4:78113800-78114400	Enhancers	Primary B cells from peripheral blood	blood
10	chr4:78113800-78120400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:78114000-78114600	Enhancers	Thymus	Thymus
12	chr4:78114200-78114400	Enhancers	Primary B cells from cord blood	blood
13	chr4:78114200-78114400	Enhancers	Primary T cells from cord blood	blood
14	chr4:78114200-78114400	Enhancers	Primary T cells fromperipheralblood	blood
15	chr4:78114200-78114400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr4:78114200-78114400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr4:78114200-78114400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr4:78114200-78114600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr4:78114200-78114600	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr4:78114200-78114600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr4:78114200-78114600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr4:78114200-78114600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:78114200-78114800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:78114200-78114800	Enhancers	Fetal Thymus	thymus
25	chr4:78114200-78115200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr4:78114200-78115600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:78114200-78116200	Enhancers	Placenta	Placenta
28	chr4:78114200-78116200	Flanking Active TSS	GM12878-XiMat	blood

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