Variant report

Variant	rs684767
Chromosome Location	chr1:210515588-210515589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210515068..210517585-chr1:210541505..210543013,2	K562	blood:
2	chr1:210515021..210516831-chr1:210522369..210524888,2	MCF-7	breast:
3	chr1:210512806..210515605-chr1:210546064..210549324,3	MCF-7	breast:
4	chr1:210513019..210515832-chr1:210545319..210548236,4	K562	blood:
5	chr1:210509334..210511204-chr1:210515301..210517705,2	K562	blood:
6	chr1:210510081..210515832-chr1:210544850..210548843,7	K562	blood:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10489387	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11119480	0.94[JPT][hapmap]
rs1883655	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs2015743	0.82[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2103691	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2143590	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2294847	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2294848	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3765867	0.85[CHB][hapmap]
rs3765873	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3765880	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3819987	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs4336853	0.85[CHB][hapmap]
rs589027	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs590883	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs642116	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6540590	0.87[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs6540591	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs655213	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs684045	1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs761172	0.90[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs764585	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs910028	0.85[ASN][1000 genomes]
rs9970232	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	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs684767	LOC148696	cis	parietal	SCAN
rs684767	ELK4	cis	parietal	SCAN
rs684767	YOD1	cis	cerebellum	SCAN
rs684767	TRAF3IP3	cis	cerebellum	SCAN
rs684767	TFF3	trans	cerebellum	SCAN
rs684767	SERTAD4	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210503200-210516800	Weak transcription	Lung	lung
2	chr1:210503600-210546800	Weak transcription	Fetal Intestine Small	intestine
3	chr1:210504400-210516400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:210506600-210515600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:210513000-210516400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:210513000-210516600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:210513000-210540400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:210513200-210516000	Enhancers	Primary hematopoietic stem cells	blood
9	chr1:210513200-210516600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:210513200-210517800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr1:210513400-210516800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:210513600-210516400	Enhancers	Dnd41	blood
13	chr1:210513600-210516600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:210513600-210517600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr1:210513600-210517800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:210513600-210517800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:210513800-210516600	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr1:210513800-210516600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:210514000-210515800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr1:210514200-210516600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:210514400-210515800	Weak transcription	Primary B cells from cord blood	blood
22	chr1:210514400-210516400	Enhancers	GM12878-XiMat	blood
23	chr1:210514400-210516600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:210514800-210515600	Enhancers	Fetal Thymus	thymus
25	chr1:210514800-210516400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:210515000-210516400	Weak transcription	Small Intestine	intestine
27	chr1:210515000-210516800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:210515000-210516800	Weak transcription	Thymus	Thymus
29	chr1:210515200-210515600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:210515200-210516200	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:210515200-210516600	Enhancers	Primary B cells from peripheral blood	blood
32	chr1:210515200-210516800	Weak transcription	Gastric	stomach
33	chr1:210515200-210517200	Enhancers	Fetal Heart	heart
34	chr1:210515400-210515600	Enhancers	Duodenum Smooth Muscle	Duodenum

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