Variant report

Variant	rs203893
Chromosome Location	chr6:28062066-28062067
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:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28061415..28063110-chr6:28078515..28080517,2	K562	blood:
2	chr6:28061840..28064330-chr6:28071288..28073320,3	K562	blood:
3	chr6:28060864..28062442-chr6:28073871..28075470,2	K562	blood:
4	chr6:28056458..28058352-chr6:28061190..28065331,3	K562	blood:
5	chr6:28055033..28059827-chr6:28060782..28064716,7	MCF-7	breast:
6	chr6:28060510..28063110-chr6:28077574..28080015,2	K562	blood:
7	chr6:28058502..28061119-chr6:28061674..28064801,3	K562	blood:
8	chr6:28060520..28063673-chr6:28071288..28074730,3	K562	blood:
9	chr6:28010916..28013781-chr6:28060247..28062544,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF165-1	chr6:28060117-28063493	NONHSAT108425

No data

Variant related genes	Relation type
ENSG00000219891	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 28 )

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

rs_ID	r²[population]
rs1071893	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1150666	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150678	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12173797	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1225592	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1225595	0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1225716	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233691	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1233708	0.95[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs149897	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs149900	0.87[ASW][hapmap];0.90[YRI][hapmap]
rs149942	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs149944	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap]
rs149945	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap]
rs149955	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs149958	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs149959	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs149961	0.90[YRI][hapmap]
rs149962	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs149965	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs149969	0.89[YRI][hapmap]
rs149970	0.82[CHB][hapmap];0.90[YRI][hapmap]
rs149972	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap]
rs149989	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap]
rs156738	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs156739	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1631552	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs172166	0.89[YRI][hapmap]
rs1770131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17711801	0.86[CEU][hapmap]
rs183244	0.91[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs188105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs203876	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs203877	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs203882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs203883	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs203884	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs203890	0.84[ASW][hapmap];0.89[YRI][hapmap]
rs203892	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2791332	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713144	0.81[CEU][hapmap]
rs476167	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs536704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7755442	0.81[CEU][hapmap]
rs9295759	0.82[CEU][hapmap]
rs9295760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393881	0.87[ASW][hapmap];0.86[YRI][hapmap]
rs9461443	0.86[CEU][hapmap]
rs9468274	0.87[ASW][hapmap];0.90[YRI][hapmap]

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:28)

SNP	Gene	Cis/trans	Tissue	Source
rs203893	ZNF323	cis	Cerebellum	GTEx
rs203893	OR2B8P	cis	Thyroid	GTEx
rs203893	ZKSCAN3	cis	parietal	SCAN
rs203893	OR2B6	cis	parietal	SCAN
rs203893	ZNF192	cis	cerebellum	SCAN
rs203893	ZSCAN31	cis	Thyroid	GTEx
rs203893	ZNF204P	cis	parietal	SCAN
rs203893	AL022393.7	cis	Artery Tibial	GTEx
rs203893	AL022393.7	cis	Nerve Tibial	GTEx
rs203893	ZNF323	cis	cerebellum	SCAN
rs203893	OR1F12	cis	Thyroid	GTEx
rs203893	AL022393.7	cis	Muscle Skeletal	GTEx
rs203893	ZNF165	cis	lymphoblastoid	seeQTL
rs203893	ZNF187	cis	parietal	SCAN
rs203893	ZNF192	cis	parietal	SCAN
rs203893	ZKSCAN3	cis	cerebellum	SCAN
rs203893	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs203893	ZNF323	cis	Temporal Cortex	GTEx
rs203893	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs203893	AL022393.7	cis	Heart Left Ventricle	GTEx
rs203893	NKAPL	cis	parietal	SCAN
rs203893	ZNF323	cis	Frontal Cortex	GTEx
rs203893	ZNF323	cis	parietal	SCAN
rs203893	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs203893	ZNF389	cis	lymphoblastoid	seeQTL
rs203893	ZNF323	cis	Brain Pons	GTEx
rs203893	ZNF187	cis	cerebellum	SCAN
rs203893	ZSCAN23	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28049600-28063000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:28053400-28064600	Strong transcription	Placenta	Placenta
3	chr6:28057800-28065800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:28058000-28064800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:28058200-28062200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:28058200-28062200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:28058200-28072200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:28058800-28072000	Weak transcription	HMEC	breast
9	chr6:28059200-28063000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:28059200-28063200	Weak transcription	Pancreas	Pancrea
11	chr6:28059200-28063400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:28059200-28066800	Weak transcription	Esophagus	oesophagus
13	chr6:28059400-28062600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:28059400-28072000	Weak transcription	Brain Substantia Nigra	brain
15	chr6:28059800-28063600	Weak transcription	Fetal Heart	heart
16	chr6:28060600-28062400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr6:28061000-28063800	Weak transcription	NHEK	skin
18	chr6:28061200-28063600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:28061200-28064600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:28061400-28072000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:28062000-28064600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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