Variant report

Variant	rs7664140
Chromosome Location	chr4:76438636-76438637
allele	G/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	HCFC1	chr4:76438148-76440349	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr4:76438236-76441446	MCF10A-Er-Src	breast:	n/a	n/a
3	RCOR1	chr4:76437777-76438680	K562	blood:	n/a	n/a
4	MAFK	chr4:76437510-76438961	K562	blood:	n/a	chr4:76438856-76438876
5	POLR2A	chr4:76438385-76440702	IMR90	lung:	n/a	n/a
6	STAT1	chr4:76438529-76438701	GM12878	blood:	n/a	n/a
7	MYC	chr4:76438273-76440163	MCF10A-Er-Src	breast:	n/a	n/a
8	CHD1	chr4:76438501-76438694	GM12878	blood:	n/a	n/a
9	IRF1	chr4:76437593-76440142	K562	blood:	n/a	chr4:76438121-76438135 chr4:76438292-76438309
10	CUX1	chr4:76437838-76438729	K562	blood:	n/a	n/a
11	POLR2A	chr4:76438260-76440663	MCF10A-Er-Src	breast:	n/a	n/a
12	MYC	chr4:76438204-76440121	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:76432863..76437584-chr4:76437624..76440912,10	MCF-7	breast:
2	chr4:76433807..76436085-chr4:76437020..76439277,2	MCF-7	breast:
3	chr4:76436258..76441363-chr4:76597157..76599917,7	K562	blood:
4	chr4:76229171..76231861-chr4:76436993..76438920,2	MCF-7	breast:
5	chr4:76435978..76441393-chr4:76648372..76651737,6	K562	blood:
6	chr4:76437150..76439919-chr4:76648856..76651737,3	K562	blood:
7	chr4:76437052..76441363-chr4:76597688..76599751,3	K562	blood:

Variant related genes	Relation type
RCHY1	TF binding region
THAP6	TF binding region
ENSG00000138768	Chromatin interaction
ENSG00000163743	Chromatin interaction
ENSG00000138757	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10029348	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10031553	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1046662	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11728327	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11729290	0.82[GIH][hapmap]
rs11729929	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11730978	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11735018	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13112378	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13145288	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1395359	0.96[CEU][hapmap]
rs1478174	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1580297	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1600100	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1817387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1841932	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1841934	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2045863	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2126855	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28507535	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867920	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2867921	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59581284	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6535523	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6815241	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6816603	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823674	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6829753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6833496	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6835579	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6841171	0.96[CEU][hapmap]
rs6841882	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7661659	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7698352	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs786688	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs9041	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9998529	0.80[GIH][hapmap]

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	nsv594687	chr4:76154064-76502748	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Strong transcription 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	27 gene(s)	inside rSNPs	diseases
2	nsv534570	chr4:76214619-76498362	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7664140	CCNI	cis	cerebellum	SCAN
rs7664140	THAP6	cis	multi-tissue	Pritchard
rs7664140	THAP6	cis	lymphoblastoid	seeQTL
rs7664140	THAP6	cis	Lymphoblastoid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76406600-76438800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:76425000-76438800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:76425400-76439000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:76435600-76438800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:76435800-76439000	Weak transcription	Gastric	stomach
6	chr4:76436000-76439400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr4:76436200-76439400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:76436200-76440600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:76436400-76439000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr4:76436400-76439200	Flanking Active TSS	Primary T cells from cord blood	blood
11	chr4:76436600-76439200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr4:76436800-76438800	Flanking Active TSS	HUVEC	blood vessel
13	chr4:76436800-76438800	Flanking Active TSS	K562	blood
14	chr4:76436800-76439000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr4:76437000-76438800	Flanking Active TSS	Thymus	Thymus
16	chr4:76437000-76438800	Enhancers	Spleen	Spleen
17	chr4:76437000-76439000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:76437000-76439000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr4:76437000-76439000	Flanking Active TSS	Dnd41	blood
20	chr4:76437000-76439200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr4:76437000-76439200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:76437000-76439200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr4:76437000-76439400	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr4:76437000-76439400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:76437000-76439600	Active TSS	Right Atrium	heart
26	chr4:76437000-76440600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:76437000-76440800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:76437200-76438800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:76437200-76438800	Flanking Active TSS	Fetal Lung	lung
30	chr4:76437200-76439200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:76437200-76439200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr4:76437400-76438800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:76437400-76439000	Flanking Active TSS	NH-A	brain
34	chr4:76437400-76440200	Active TSS	Stomach Smooth Muscle	stomach
35	chr4:76437400-76440600	Active TSS	Psoas Muscle	Psoas
36	chr4:76437400-76440800	Active TSS	A549	lung
37	chr4:76437600-76438800	Flanking Active TSS	Fetal Thymus	thymus
38	chr4:76437600-76439200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr4:76437600-76440200	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr4:76437600-76440400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:76437600-76440400	Active TSS	Aorta	Aorta
42	chr4:76437600-76440800	Active TSS	Colonic Mucosa	Colon
43	chr4:76437800-76438800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:76437800-76438800	Weak transcription	Esophagus	oesophagus
45	chr4:76437800-76438800	Weak transcription	Pancreas	Pancrea
46	chr4:76437800-76440400	Active TSS	Left Ventricle	heart
47	chr4:76437800-76440600	Active TSS	H1 Cell Line	embryonic stem cell
48	chr4:76437800-76440600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:76437800-76440600	Active TSS	Right Ventricle	heart
50	chr4:76438000-76438800	Enhancers	H9 Cell Line	embryonic stem cell

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