Variant report

Variant	rs1778484
Chromosome Location	chr6:28240798-28240799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28239901..28245005-chr6:28300469..28305210,5	K562	blood:
2	chr6:28240382..28242632-chr6:28248065..28250741,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction
ENSG00000137338	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1052215	0.91[ASW][hapmap];0.91[CHB][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap]
rs1150668	0.90[JPT][hapmap]
rs1150694	0.90[JPT][hapmap]
rs1150705	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1150707	0.91[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs1150709	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1150711	0.83[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.95[ASN][1000 genomes]
rs1150716	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1150718	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1150721	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1150724	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1150726	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12214383	0.91[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1225618	0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs1225710	0.91[ASW][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap]
rs1225715	0.85[CHD][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs1233660	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1233713	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13408	0.91[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1531681	0.91[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1654774	0.82[CHD][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap]
rs1736891	0.91[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs1736895	0.91[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1997660	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2021826	0.90[JPT][hapmap]
rs203869	0.90[JPT][hapmap]
rs203878	0.91[ASW][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap]
rs213238	0.85[JPT][hapmap]
rs213240	0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap]
rs2142730	0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2394049	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2622320	0.89[JPT][hapmap]
rs2622322	0.90[JPT][hapmap]
rs2791333	0.81[ASW][hapmap];0.81[CHD][hapmap];0.94[MKK][hapmap];0.80[TSI][hapmap]
rs2859348	0.86[CHB][hapmap]
rs4713158	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs707907	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7206	0.82[ASW][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs853683	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs853684	0.91[ASW][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs853690	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs853693	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9301	0.90[ASW][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs9468333	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[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	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:22)

SNP	Gene	Cis/trans	Tissue	Source
rs1778484	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs1778484	HIST1H4C	cis	parietal	SCAN
rs1778484	BTN3A1	cis	parietal	SCAN
rs1778484	RP5-874C20.3	cis	Thyroid	GTEx
rs1778484	ZNF187	cis	cerebellum	SCAN
rs1778484	ZNF323	cis	parietal	SCAN
rs1778484	ZKSCAN3	cis	cerebellum	SCAN
rs1778484	AL022393.7	cis	Nerve Tibial	GTEx
rs1778484	ZNF192	cis	cerebellum	SCAN
rs1778484	ZSCAN23	cis	cerebellum	SCAN
rs1778484	ZNF323	cis	cerebellum	SCAN
rs1778484	NKAPL	cis	parietal	SCAN
rs1778484	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs1778484	ZSCAN31	cis	Thyroid	GTEx
rs1778484	GRIN3A	trans	cerebellum	SCAN
rs1778484	AL022393.7	cis	Muscle Skeletal	GTEx
rs1778484	ZKSCAN3	cis	parietal	SCAN
rs1778484	ZSCAN23	cis	parietal	SCAN
rs1778484	AL022393.7	cis	Heart Left Ventricle	GTEx
rs1778484	ZSCAN31	cis	lung	GTEx
rs1778484	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs1778484	HIST1H1D	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28235400-28249000	Weak transcription	Small Intestine	intestine
2	chr6:28235600-28243400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:28235600-28249000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:28235600-28249000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:28236200-28241800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:28236200-28247400	Weak transcription	Stomach Mucosa	stomach
7	chr6:28236200-28248000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:28236200-28249400	Weak transcription	Fetal Heart	heart
9	chr6:28236400-28242000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:28237400-28241600	Weak transcription	GM12878-XiMat	blood
11	chr6:28237400-28245800	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:28237400-28249000	Weak transcription	Psoas Muscle	Psoas
13	chr6:28237600-28248800	Weak transcription	A549	lung
14	chr6:28238000-28245600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:28238000-28248800	Weak transcription	Hela-S3	cervix
16	chr6:28238200-28245200	Strong transcription	Fetal Intestine Large	intestine
17	chr6:28238800-28244000	Strong transcription	Ovary	ovary
18	chr6:28238800-28245400	Strong transcription	Fetal Stomach	stomach
19	chr6:28238800-28245600	Strong transcription	Primary T cells from cord blood	blood
20	chr6:28238800-28245800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr6:28238800-28245800	Strong transcription	Stomach Smooth Muscle	stomach
22	chr6:28238800-28246000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:28239200-28241200	Strong transcription	Right Ventricle	heart
24	chr6:28239200-28242000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:28239200-28242400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:28239200-28242600	Strong transcription	Fetal Intestine Small	intestine
27	chr6:28239200-28243800	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr6:28239200-28244800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:28239200-28245000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:28239200-28245000	Strong transcription	Spleen	Spleen
31	chr6:28239200-28245200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr6:28239200-28245200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:28239200-28245200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:28239200-28245200	Strong transcription	Lung	lung
35	chr6:28239200-28245400	Strong transcription	Brain Anterior Caudate	brain
36	chr6:28239200-28245400	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr6:28239200-28245600	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:28239200-28245600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr6:28239200-28246000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:28239200-28246000	Strong transcription	Colon Smooth Muscle	Colon
41	chr6:28239400-28245000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:28239400-28245400	Strong transcription	Primary hematopoietic stem cells	blood
43	chr6:28239400-28246000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:28239600-28241000	Strong transcription	Esophagus	oesophagus
45	chr6:28239600-28241200	Strong transcription	Aorta	Aorta
46	chr6:28239600-28241600	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr6:28239600-28241600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:28239600-28241800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:28239600-28241800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:28239600-28241800	Strong transcription	Gastric	stomach

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