Variant report

Variant	rs4143678
Chromosome Location	chr6:44365851-44365852
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:44354045..44356873-chr6:44363627..44365870,2	MCF-7	breast:
2	chr6:44364744..44367505-chr6:44368641..44372251,3	K562	blood:
3	chr6:44357790..44359510-chr6:44364205..44366302,2	K562	blood:

Variant related genes	Relation type
ENSG00000096401	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10807300	0.84[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes]
rs11961973	0.84[CHB][hapmap]
rs1293205	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1293208	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1296018	0.95[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1952979	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2273667	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs2297331	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2297333	0.85[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34753552	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711781	0.85[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs475426	0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs525043	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs526851	0.85[ASN][1000 genomes]
rs532492	0.81[EUR][1000 genomes]
rs545455	0.95[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs548342	0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.99[MKK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs557470	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs559035	0.95[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs564988	0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs67182313	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6918742	0.81[CHB][hapmap]
rs6923521	0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6942323	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs864127	0.84[CHB][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes]
rs9395017	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs9462984	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9462985	0.83[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9462989	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9472273	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019145	chr6:44313576-44421440	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4143678	CDC5L	cis	parietal	SCAN
rs4143678	RUNX2	cis	cerebellum	SCAN
rs4143678	GPR115	cis	cerebellum	SCAN
rs4143678	CD2AP	cis	cerebellum	SCAN
rs4143678	UNC5CL	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44356400-44393800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:44357200-44376200	Weak transcription	Stomach Mucosa	stomach
3	chr6:44357400-44367000	Strong transcription	HSMM	muscle
4	chr6:44357400-44367200	Strong transcription	Fetal Muscle Leg	muscle
5	chr6:44357600-44370200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:44357600-44377600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:44357600-44383200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:44357600-44388200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:44357800-44367000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr6:44357800-44367200	Strong transcription	Placenta	Placenta
11	chr6:44357800-44378200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:44358000-44366200	Strong transcription	NH-A	brain
13	chr6:44358000-44366800	Strong transcription	HMEC	breast
14	chr6:44358000-44367400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr6:44358000-44369200	Strong transcription	Osteobl	bone
16	chr6:44358000-44384800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:44358000-44385600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:44358000-44385600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:44358000-44385800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr6:44358000-44386000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:44358200-44369200	Strong transcription	Hela-S3	cervix
22	chr6:44358200-44378000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr6:44358200-44381800	Strong transcription	Fetal Thymus	thymus
24	chr6:44358200-44385600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr6:44358400-44367600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:44358400-44368400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:44358400-44368400	Strong transcription	Adipose Nuclei	Adipose
28	chr6:44358400-44378400	Strong transcription	K562	blood
29	chr6:44358400-44385200	Strong transcription	Dnd41	blood
30	chr6:44358400-44386000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:44358400-44403800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:44358600-44367200	Strong transcription	Thymus	Thymus
33	chr6:44358600-44369200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr6:44358600-44378600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:44358600-44381800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:44358800-44366400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:44358800-44367000	Strong transcription	Lung	lung
38	chr6:44358800-44369400	Strong transcription	Fetal Stomach	stomach
39	chr6:44358800-44385600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr6:44359000-44366000	Strong transcription	Ovary	ovary
41	chr6:44359000-44366800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:44359000-44367800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:44359000-44369200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:44359000-44369400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:44359200-44366000	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr6:44359200-44366000	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr6:44359200-44366000	Strong transcription	Spleen	Spleen
48	chr6:44359200-44366200	Strong transcription	HSMMtube	muscle
49	chr6:44359200-44366400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:44359200-44366600	Strong transcription	Muscle Satellite Cultured Cells	--

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