Variant report

Variant	rs6447978
Chromosome Location	chr4:20736742-20736743
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	chr4:20736248..20737799-chr4:20738056..20739802,2	MCF-7	breast:
2	chr4:20736150..20738048-chr4:20747130..20748840,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10017693	0.85[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10018931	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10022322	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10024002	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10025286	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10034054	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10084802	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10805219	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10938801	0.81[MKK][hapmap];0.82[YRI][hapmap]
rs11941041	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11944886	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12152652	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12331966	0.95[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12641748	0.86[CHB][hapmap]
rs12644782	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12650007	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16869886	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16869889	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1985322	0.88[ASW][hapmap];0.86[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2052775	0.95[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2114472	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2114473	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2162413	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2288308	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2322688	0.94[ASW][hapmap];0.87[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28524474	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28637181	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28714128	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28788006	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3764964	0.94[ASW][hapmap];0.95[CEU][hapmap];0.80[GIH][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3764965	0.89[YRI][hapmap]
rs3764966	0.95[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3815872	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3816874	0.83[YRI][hapmap]
rs4414951	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4431223	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4510461	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4640668	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55847423	0.95[ASN][1000 genomes]
rs57740160	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59335491	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62410159	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6447974	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6447975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6447976	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6447982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6811030	0.89[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6811505	1.00[CEU][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6817475	0.87[CEU][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6831295	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6831516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7438098	0.86[EUR][1000 genomes]
rs7655154	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7660006	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7666288	0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7673805	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7674453	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7681691	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7685481	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7689421	0.80[YRI][hapmap]
rs7694208	0.80[YRI][hapmap]
rs7696618	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs990206	0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9995438	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9995697	0.95[CEU][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv869522	chr4:20724433-20938248	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6447978	PACRGL	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20703000-20741400	Weak transcription	Stomach Mucosa	stomach
2	chr4:20703200-20741000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:20706800-20738600	Weak transcription	Psoas Muscle	Psoas
4	chr4:20707200-20739400	Weak transcription	HepG2	liver
5	chr4:20715400-20738600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:20715400-20739400	Weak transcription	Osteobl	bone
7	chr4:20718000-20738600	Weak transcription	NHDF-Ad	bronchial
8	chr4:20718200-20738400	Weak transcription	Fetal Heart	heart
9	chr4:20721800-20737200	Strong transcription	Liver	Liver
10	chr4:20723000-20738400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:20724200-20737000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr4:20724200-20738800	Weak transcription	Gastric	stomach
13	chr4:20724200-20738800	Weak transcription	Small Intestine	intestine
14	chr4:20724400-20737000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:20724400-20737000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:20724400-20738400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:20724400-20738800	Weak transcription	Esophagus	oesophagus
18	chr4:20724400-20738800	Weak transcription	HMEC	breast
19	chr4:20724400-20739000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:20724400-20739400	Weak transcription	Fetal Thymus	thymus
21	chr4:20724400-20739400	Weak transcription	Thymus	Thymus
22	chr4:20724400-20739400	Weak transcription	Spleen	Spleen
23	chr4:20724400-20740000	Weak transcription	GM12878-XiMat	blood
24	chr4:20724600-20739200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr4:20724600-20742000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr4:20724800-20736800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:20724800-20738600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr4:20724800-20738600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:20724800-20738600	Weak transcription	Fetal Brain Male	brain
30	chr4:20724800-20738800	Weak transcription	Brain Substantia Nigra	brain
31	chr4:20724800-20741600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:20725000-20738200	Weak transcription	NHEK	skin
33	chr4:20725000-20738400	Weak transcription	A549	lung
34	chr4:20725000-20740600	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:20725000-20753000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:20725200-20739200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:20725600-20738400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:20725600-20740000	Weak transcription	Brain Anterior Caudate	brain
39	chr4:20726000-20738800	Weak transcription	Right Ventricle	heart
40	chr4:20726000-20740000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr4:20726200-20740400	Weak transcription	Colonic Mucosa	Colon
42	chr4:20726600-20738600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr4:20727200-20736800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr4:20728400-20737200	Strong transcription	Primary T cells from cord blood	blood
45	chr4:20728800-20738200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr4:20729800-20738600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:20730200-20738800	Weak transcription	Fetal Stomach	stomach
48	chr4:20730600-20739000	Weak transcription	Placenta	Placenta
49	chr4:20730600-20739600	Weak transcription	HUVEC	blood vessel
50	chr4:20730600-20757600	Weak transcription	HSMM	muscle

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