Variant report

Variant	rs1150694
Chromosome Location	chr6:28175153-28175154
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28154956..28156603-chr6:28174738..28177213,2	K562	blood:
2	chr6:28170074..28175450-chr6:28180913..28183647,5	K562	blood:
3	chr6:28174435..28176569-chr6:28303412..28304973,2	MCF-7	breast:
4	chr6:28174526..28176071-chr6:28185476..28187807,2	MCF-7	breast:
5	chr6:28109035..28111134-chr6:28175130..28176632,2	K562	blood:
6	chr6:28170099..28172681-chr6:28173612..28177819,3	K562	blood:
7	chr6:28174974..28177419-chr6:28322626..28324224,2	K562	blood:
8	chr6:28172570..28175998-chr6:28183959..28188768,7	K562	blood:
9	chr6:28154709..28159711-chr6:28172250..28177968,6	K562	blood:
10	chr6:28174164..28176650-chr6:28369447..28371283,2	K562	blood:
11	chr6:28166299..28169743-chr6:28173090..28175496,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198315	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000218016	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1005125	1.00[YRI][hapmap]
rs1052215	1.00[YRI][hapmap]
rs1150668	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1150670	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1150679	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150686	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1150690	0.94[ASN][1000 genomes]
rs1150705	0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs1150707	0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1150709	0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1150711	0.90[JPT][hapmap]
rs1150716	0.85[EUR][1000 genomes]
rs1150718	1.00[YRI][hapmap]
rs1150721	1.00[YRI][hapmap]
rs1150724	1.00[YRI][hapmap]
rs1150726	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs12214383	0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1225618	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1225710	0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1225715	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1233660	0.82[AFR][1000 genomes]
rs1233713	0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12530158	0.82[JPT][hapmap]
rs13408	0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs149956	0.80[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs149976	0.90[JPT][hapmap]
rs1531681	0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1654774	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1736891	0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1736895	0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1778484	0.90[JPT][hapmap]
rs1997660	1.00[YRI][hapmap]
rs2021826	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs203869	0.84[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs203878	0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs213240	0.85[AFR][1000 genomes]
rs2142730	0.85[EUR][1000 genomes]
rs2394049	0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2622320	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2622322	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2791333	0.82[JPT][hapmap];0.96[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34024998	0.80[EUR][1000 genomes]
rs707907	1.00[YRI][hapmap]
rs7206	0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs853683	1.00[YRI][hapmap]
rs853684	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs853690	1.00[YRI][hapmap]
rs853693	1.00[YRI][hapmap]
rs9301	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9468333	1.00[YRI][hapmap]

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	nsv883514	chr6:28155418-28185726	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv883515	chr6:28156476-28181675	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv883516	chr6:28156476-28185726	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs1150694	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs1150694	ZNF165	cis	Artery Tibial	GTEx
rs1150694	ZSCAN23	cis	Artery Tibial	GTEx
rs1150694	AL022393.7	cis	lung	GTEx
rs1150694	AL022393.7	cis	Nerve Tibial	GTEx
rs1150694	ZSCAN31	cis	lung	GTEx
rs1150694	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs1150694	ZSCAN31	cis	Thyroid	GTEx
rs1150694	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs1150694	AL022393.7	cis	Artery Tibial	GTEx
rs1150694	ZSCAN23	cis	lung	GTEx
rs1150694	AL022393.7	cis	Artery Aorta	GTEx
rs1150694	RP5-874C20.3	cis	Thyroid	GTEx
rs1150694	ZNF165	cis	Nerve Tibial	GTEx
rs1150694	AL022393.7	cis	Esophagus Muscularis	GTEx
rs1150694	ZSCAN23	cis	Muscle Skeletal	GTEx
rs1150694	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1150694	AL022393.7	cis	Muscle Skeletal	GTEx
rs1150694	AL022393.7	cis	Heart Left Ventricle	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28174000-28176400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:28174200-28176400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
3	chr6:28174600-28176400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:28174600-28176600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:28174800-28175200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:28174800-28175200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:28174800-28175200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
8	chr6:28174800-28175200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:28174800-28175200	Bivalent Enhancer	Colonic Mucosa	Colon
10	chr6:28174800-28175200	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr6:28174800-28175200	Bivalent Enhancer	Fetal Kidney	kidney
12	chr6:28174800-28175200	Bivalent Enhancer	Fetal Lung	lung
13	chr6:28174800-28175200	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr6:28174800-28175200	Bivalent Enhancer	Fetal Stomach	stomach
15	chr6:28174800-28175200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr6:28174800-28175200	Bivalent/Poised TSS	GM12878-XiMat	blood
17	chr6:28174800-28175200	Bivalent Enhancer	HSMMtube	muscle
18	chr6:28174800-28175400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:28174800-28175400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
20	chr6:28174800-28175400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
21	chr6:28174800-28175400	Bivalent Enhancer	Stomach Mucosa	stomach
22	chr6:28174800-28175800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:28174800-28175800	Bivalent/Poised TSS	NHEK	skin
24	chr6:28174800-28176200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:28174800-28176200	Bivalent Enhancer	Small Intestine	intestine
26	chr6:28174800-28176400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
27	chr6:28174800-28176400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
28	chr6:28174800-28176400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
29	chr6:28174800-28176400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr6:28174800-28176400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
31	chr6:28174800-28176400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
32	chr6:28174800-28176400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
33	chr6:28174800-28176400	Bivalent/Poised TSS	NHLF	lung
34	chr6:28174800-28176600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
35	chr6:28174800-28176600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:28175000-28175200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:28175000-28175200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:28175000-28175200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:28175000-28175200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:28175000-28175200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:28175000-28175200	Bivalent/Poised TSS	Adipose Nuclei	Adipose
42	chr6:28175000-28175200	Flanking Active TSS	Placenta	Placenta
43	chr6:28175000-28175200	Bivalent Enhancer	Psoas Muscle	Psoas
44	chr6:28175000-28175200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
45	chr6:28175000-28175200	Active TSS	A549	lung
46	chr6:28175000-28175200	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
47	chr6:28175000-28175400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr6:28175000-28175400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:28175000-28175400	Bivalent Enhancer	Fetal Heart	heart
50	chr6:28175000-28175400	Bivalent/Poised TSS	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links