Variant report

Variant	rs6835579
Chromosome Location	chr4:76436453-76436454
allele	A/G
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	STAT3	chr4:76436426-76436565	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:76436381-76436455	ProgFib	skin:	n/a	n/a
3	FOS	chr4:76436209-76436517	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr4:76436178-76436532	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:76422807..76425261-chr4:76435739..76438350,2	MCF-7	breast:
2	chr4:76435271..76437331-chr4:76452184..76454371,2	K562	blood:
3	chr4:76436258..76441363-chr4:76597157..76599917,7	K562	blood:
4	chr4:76435978..76441393-chr4:76648372..76651737,6	K562	blood:
5	chr4:76432863..76437584-chr4:76437624..76440912,10	MCF-7	breast:

Variant related genes	Relation type
THAP6	TF binding region
RCHY1	TF binding region
ENSG00000174796	Chromatin interaction
ENSG00000138757	Chromatin interaction
ENSG00000163743	Chromatin interaction
ENSG00000138768	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10029348	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10031553	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1046662	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11728327	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11729929	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11730978	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735018	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112378	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145288	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395359	0.96[CEU][hapmap]
rs1478174	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1580297	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1600100	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1817387	1.00[CEU][hapmap];0.95[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];0.98[ASN][1000 genomes]
rs1841932	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1841934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045863	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126855	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28507535	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867920	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2867921	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59581284	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6535523	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6815241	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816603	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833496	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841171	0.96[CEU][hapmap]
rs6841882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664140	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]
rs7698352	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs786688	0.96[CEU][hapmap]
rs9041	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6835579	THAP6	cis	Lymphoblastoid	GTEx
rs6835579	THAP6	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76395800-76437000	Weak transcription	Aorta	Aorta
2	chr4:76395800-76437000	Weak transcription	Lung	lung
3	chr4:76395800-76437000	Weak transcription	Pancreas	Pancrea
4	chr4:76396200-76437000	Weak transcription	Esophagus	oesophagus
5	chr4:76397800-76437000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:76398800-76437200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:76400600-76437000	Weak transcription	Spleen	Spleen
8	chr4:76406000-76436600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:76406600-76438800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:76408000-76436600	Weak transcription	Hela-S3	cervix
11	chr4:76410000-76437200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:76416600-76437000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:76417600-76436800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:76421400-76437000	Weak transcription	Stomach Mucosa	stomach
15	chr4:76424800-76437000	Weak transcription	Psoas Muscle	Psoas
16	chr4:76424800-76437000	Weak transcription	NHLF	lung
17	chr4:76425000-76437000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:76425000-76438800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:76425400-76437000	Weak transcription	Right Ventricle	heart
20	chr4:76425400-76439000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:76425600-76436600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:76426000-76436800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:76427800-76437200	Weak transcription	Fetal Stomach	stomach
24	chr4:76428400-76437400	Weak transcription	A549	lung
25	chr4:76428600-76436600	Weak transcription	Brain Germinal Matrix	brain
26	chr4:76429000-76437000	Weak transcription	Fetal Intestine Small	intestine
27	chr4:76430400-76437000	Weak transcription	HSMMtube	muscle
28	chr4:76430600-76436600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:76430600-76436800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:76430600-76437000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:76430600-76437000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:76430600-76437000	Weak transcription	Thymus	Thymus
33	chr4:76430800-76436800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:76430800-76437200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr4:76430800-76438200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr4:76431000-76436800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:76431000-76437000	Weak transcription	Fetal Muscle Leg	muscle
38	chr4:76431200-76436600	Weak transcription	Fetal Brain Female	brain
39	chr4:76431200-76436800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:76431200-76437200	Weak transcription	Colonic Mucosa	Colon
41	chr4:76431400-76437000	Weak transcription	NH-A	brain
42	chr4:76433600-76436600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr4:76433600-76436800	Weak transcription	Fetal Kidney	kidney
44	chr4:76433600-76437000	Weak transcription	Fetal Thymus	thymus
45	chr4:76434000-76437000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:76434000-76437200	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr4:76434200-76436600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:76434200-76437000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr4:76434200-76437200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr4:76434200-76437200	Enhancers	Primary T helper cells fromperipheralblood	blood

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