Variant report

Variant	rs427348
Chromosome Location	chr6:28058365-28058366
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28058269-28058400	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr6:28057384-28059244	HepG2	liver:	n/a	n/a
3	SETDB1	chr6:28055578-28058467	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28049008..28053394-chr6:28054919..28058473,6	MCF-7	breast:
2	chr6:28056458..28058626-chr6:28119915..28122214,2	K562	blood:
3	chr6:28047913..28051449-chr6:28052832..28058819,8	K562	blood:

Variant related genes	Relation type
ZSCAN12P1	TF binding region
ENSG00000272009	Chromatin interaction
ENSG00000197279	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1150672	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1150674	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1150676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1150680	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1150683	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1150684	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1225593	0.92[YRI][hapmap]
rs1225594	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1225709	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1225711	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233784	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1237873	1.00[ASW][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes]
rs1416997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1480646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs149898	0.85[YRI][hapmap]
rs149957	1.00[ASW][hapmap];0.91[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1529749	1.00[CEU][hapmap]
rs156741	1.00[ASW][hapmap]
rs156742	1.00[ASW][hapmap]
rs1613149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1619221	0.92[YRI][hapmap]
rs1654777	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1654778	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs169432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs169433	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs172164	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs175955	0.92[YRI][hapmap]
rs1770130	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1770132	1.00[YRI][hapmap]
rs1770133	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17709097	1.00[CEU][hapmap];0.94[GIH][hapmap]
rs17709109	1.00[CEU][hapmap]
rs17709523	1.00[CEU][hapmap]
rs17765491	1.00[CEU][hapmap]
rs1871695	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs200970	1.00[ASW][hapmap]
rs203865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203868	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203871	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs203874	1.00[YRI][hapmap]
rs203875	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203881	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203885	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203891	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs203894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2394044	1.00[CEU][hapmap]
rs2622318	0.92[YRI][hapmap]
rs2622321	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs276364	1.00[ASW][hapmap]
rs2791334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs370266	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs392665	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41375446	1.00[CEU][hapmap];0.94[GIH][hapmap]
rs425159	0.85[YRI][hapmap]
rs539474	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57349346	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58909320	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73740569	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73740570	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73742609	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9348782	1.00[CEU][hapmap]
rs9348790	1.00[CEU][hapmap]
rs9348791	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9348795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9357055	1.00[CEU][hapmap]
rs9357056	1.00[CEU][hapmap]
rs9366714	0.87[ASN][1000 genomes]
rs9368545	1.00[CEU][hapmap]
rs9368562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9380042	1.00[CEU][hapmap]
rs9393873	1.00[CEU][hapmap]
rs9393874	1.00[CEU][hapmap]
rs9393879	1.00[CEU][hapmap];0.94[GIH][hapmap]
rs9393905	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[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	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs427348	Hs.158943	cis	multi-tissue	Pritchard
rs427348	ZNF165	cis	lymphoblastoid	seeQTL
rs427348	ZNF165	cis	multi-tissue	Pritchard
rs427348	HIST1H3H	cis	lymphoblastoid	seeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28049600-28058600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr6:28049600-28058600	Weak transcription	Brain Substantia Nigra	brain
3	chr6:28049600-28059200	Weak transcription	Fetal Brain Male	brain
4	chr6:28049600-28063000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:28049800-28058600	Weak transcription	Brain Germinal Matrix	brain
6	chr6:28049800-28058600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:28050800-28061200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:28051200-28058600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:28053200-28059200	ZNF genes & repeats	Liver	Liver
10	chr6:28053400-28064600	Strong transcription	Placenta	Placenta
11	chr6:28054200-28058600	Weak transcription	Brain Angular Gyrus	brain
12	chr6:28054200-28058600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:28054200-28058600	Weak transcription	Ovary	ovary
14	chr6:28054200-28058600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:28054600-28058600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
16	chr6:28054800-28058400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
17	chr6:28055000-28059200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
18	chr6:28055200-28059600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
19	chr6:28055400-28058400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:28055400-28058400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
21	chr6:28055400-28058600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:28055400-28058800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
23	chr6:28055400-28058800	ZNF genes & repeats	HMEC	breast
24	chr6:28055400-28059400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
25	chr6:28055400-28059800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:28055600-28059200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:28055600-28059200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
28	chr6:28056000-28058600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr6:28056200-28059400	Weak transcription	HepG2	liver
30	chr6:28056600-28058400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:28057000-28058600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:28057200-28058400	Weak transcription	Hela-S3	cervix
33	chr6:28057200-28058600	Weak transcription	Brain Anterior Caudate	brain
34	chr6:28057200-28058600	Weak transcription	Fetal Kidney	kidney
35	chr6:28057200-28058600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr6:28057200-28058600	Weak transcription	Fetal Stomach	stomach
37	chr6:28057200-28058600	Weak transcription	Left Ventricle	heart
38	chr6:28057200-28058600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr6:28057200-28058600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr6:28057200-28058800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:28057200-28058800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:28057200-28058800	Weak transcription	Aorta	Aorta
43	chr6:28057200-28058800	Weak transcription	Gastric	stomach
44	chr6:28057200-28058800	Weak transcription	Lung	lung
45	chr6:28057200-28058800	Weak transcription	Pancreas	Pancrea
46	chr6:28057200-28059000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr6:28057400-28058600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:28057400-28059400	ZNF genes & repeats	Fetal Intestine Large	intestine
49	chr6:28057800-28058600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr6:28057800-28058800	Weak transcription	Dnd41	blood

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