Variant report

Variant	rs4975193
Chromosome Location	chr4:129980630-129980631
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	chr4:129977804..129979705-chr4:129980328..129983022,2	K562	blood:
2	chr4:129979538..129981345-chr4:129981662..129983621,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10002332	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10032000	0.93[CEU][hapmap];0.86[JPT][hapmap]
rs1030831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.80[LWK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1037147	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11934740	0.81[TSI][hapmap]
rs12171333	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13109003	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130762	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1374491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1596963	0.87[ASN][1000 genomes]
rs1668289	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs1699379	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699380	0.82[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1699385	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699387	0.82[ASW][hapmap];0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1699388	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699389	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1699393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1699394	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17014265	0.88[CHB][hapmap]
rs1709419	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1709422	0.86[YRI][hapmap]
rs1756012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1757924	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.80[LWK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757927	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757928	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757930	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1757935	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1757936	0.82[CHD][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes]
rs1854773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1854774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs189235	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2034498	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2083634	1.00[CEU][hapmap]
rs2198042	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2597836	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2655310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs280594	0.85[YRI][hapmap]
rs280603	1.00[CEU][hapmap];0.83[JPT][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs280604	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3105369	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3113407	0.93[CEU][hapmap];0.81[JPT][hapmap]
rs3113489	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3113490	0.81[YRI][hapmap];0.88[AMR][1000 genomes]
rs318502	0.86[JPT][hapmap]
rs318503	0.83[JPT][hapmap]
rs318536	0.93[CEU][hapmap];0.86[JPT][hapmap]
rs318543	0.93[CEU][hapmap];0.86[JPT][hapmap]
rs318552	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs337263	0.89[ASW][hapmap];0.93[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs337270	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs337275	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs337277	0.82[ASW][hapmap];0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs337278	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35006492	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs389376	0.89[ASW][hapmap];0.93[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs390260	0.82[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs391396	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs395864	0.93[CEU][hapmap];0.88[CHB][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs426521	0.93[CEU][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4394010	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs445294	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4466058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs474667	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs474794	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs487233	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs487501	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4975194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517659	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57501568	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs576492	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58689608	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6534707	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66921209	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6824219	0.80[TSI][hapmap]
rs7655841	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7671508	0.82[CHD][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes]
rs789982	0.82[CHD][hapmap];0.82[LWK][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv522694	chr4:129862073-129994690	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4975193	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs4975193	C4orf33	cis	Artery Tibial	GTEx
rs4975193	C4orf33	cis	lymphoblastoid	seeQTL
rs4975193	C4orf33	cis	Whole Blood	GTEx
rs4975193	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs4975193	ZNF226	trans	cerebellum	SCAN
rs4975193	SCLT1	cis	cerebellum	SCAN
rs4975193	SCLT1	Cis_1M	lymphoblastoid	RTeQTL
rs4975193	C4orf33	cis	parietal	SCAN
rs4975193	C4orf33	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129945600-129981800	Weak transcription	Thymus	Thymus
2	chr4:129977200-130000600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:129977400-129981600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:129977400-129981600	Weak transcription	Aorta	Aorta
5	chr4:129977400-129981600	Weak transcription	Gastric	stomach
6	chr4:129977400-129981800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:129977400-129981800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:129977400-129982000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:129977400-129982000	Weak transcription	Ovary	ovary
10	chr4:129977400-129982000	Weak transcription	Pancreas	Pancrea
11	chr4:129979400-129983800	Weak transcription	NH-A	brain
12	chr4:129980000-129983000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:129980000-129986000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr4:129980200-129985200	ZNF genes & repeats	Adipose Nuclei	Adipose
15	chr4:129980200-129985400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
16	chr4:129980200-129986200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:129980400-129985000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
18	chr4:129980400-129985600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin

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