Variant report

Variant	rs10417974
Chromosome Location	chr19:19222070-19222071
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19221369..19226288-chr19:19228208..19232737,8	K562	blood:
2	chr19:19191060..19192627-chr19:19221206..19223670,2	K562	blood:
3	chr19:19221106..19223983-chr19:19247665..19249535,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064545	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1007483	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10221504	0.94[EUR][1000 genomes]
rs10405635	0.85[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.96[EUR][1000 genomes]
rs10409164	0.92[EUR][1000 genomes]
rs10410451	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs10410568	0.86[AFR][1000 genomes]
rs10414676	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs10416783	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10421019	0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs10422906	0.89[EUR][1000 genomes]
rs10423742	0.94[ASW][hapmap];0.93[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1079543	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10854005	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11666340	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11666627	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670204	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11729	0.82[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs12016	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12975676	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12979565	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12979841	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12985799	0.94[ASW][hapmap];0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1859267	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2012318	1.00[ASW][hapmap];0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2158320	0.90[EUR][1000 genomes]
rs2240094	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2269806	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2285851	0.86[CEU][hapmap];0.85[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2872394	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap]
rs3180770	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4808179	0.90[EUR][1000 genomes]
rs4808184	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4808895	0.85[CEU][hapmap]
rs4808906	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4808907	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4808911	0.92[EUR][1000 genomes]
rs4808913	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4808916	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4808923	0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs6511010	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6511014	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6511015	0.92[EUR][1000 genomes]
rs6511017	0.92[EUR][1000 genomes]
rs6511018	1.00[ASW][hapmap];0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6511021	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs7248399	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7248651	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7248771	0.84[AFR][1000 genomes]
rs7250131	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7253244	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7256648	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7257635	0.85[EUR][1000 genomes]
rs7259609	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs756791	0.81[EUR][1000 genomes]
rs756792	0.84[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs757220	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs757221	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8103431	0.92[EUR][1000 genomes]
rs8104799	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8107710	0.87[EUR][1000 genomes]
rs8110629	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap]
rs8111634	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs929215	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.80[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	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10417974	ZNF14	cis	parietal	SCAN
rs10417974	SFRS14	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19180600-19245600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:19180600-19248400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:19194600-19229400	Weak transcription	Dnd41	blood
4	chr19:19197400-19222600	Weak transcription	GM12878-XiMat	blood
5	chr19:19203800-19245600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr19:19206600-19229600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr19:19209000-19223600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:19210200-19230200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:19212600-19229600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:19212600-19240800	Weak transcription	Aorta	Aorta
11	chr19:19216600-19223200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:19217000-19236800	Weak transcription	Hela-S3	cervix
13	chr19:19217200-19224000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:19217200-19247800	Weak transcription	Right Atrium	heart
15	chr19:19217400-19224000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr19:19217400-19229400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr19:19217400-19229600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr19:19217400-19229600	Weak transcription	NHLF	lung
19	chr19:19219000-19223600	Weak transcription	K562	blood
20	chr19:19219200-19229400	Weak transcription	Pancreas	Pancrea
21	chr19:19219400-19229400	Weak transcription	Lung	lung
22	chr19:19219400-19229600	Weak transcription	Brain Hippocampus Middle	brain
23	chr19:19219400-19229600	Weak transcription	Left Ventricle	heart
24	chr19:19219800-19229400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:19219800-19230000	Weak transcription	Brain Substantia Nigra	brain
26	chr19:19220200-19224800	Enhancers	Fetal Muscle Leg	muscle
27	chr19:19220400-19247800	Weak transcription	Psoas Muscle	Psoas
28	chr19:19220600-19222400	Enhancers	Primary T cells fromperipheralblood	blood
29	chr19:19220600-19222800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr19:19220800-19223800	Weak transcription	HepG2	liver
31	chr19:19220800-19223800	Weak transcription	HSMM	muscle
32	chr19:19220800-19242800	Weak transcription	Osteobl	bone
33	chr19:19221000-19222400	Enhancers	Placenta	Placenta
34	chr19:19221000-19223000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr19:19221000-19224200	Enhancers	Primary B cells from peripheral blood	blood
36	chr19:19221200-19222200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr19:19221200-19222400	Enhancers	Gastric	stomach
38	chr19:19221200-19223200	Enhancers	Adipose Nuclei	Adipose
39	chr19:19221200-19224000	Enhancers	Fetal Lung	lung
40	chr19:19221400-19223000	Weak transcription	Primary T cells from cord blood	blood
41	chr19:19221400-19230200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr19:19221400-19232600	Weak transcription	HSMMtube	muscle
43	chr19:19221600-19222200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:19221600-19222200	Enhancers	Fetal Intestine Small	intestine
45	chr19:19221600-19222200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr19:19221600-19222800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:19221600-19222800	Enhancers	Duodenum Mucosa	Duodenum
48	chr19:19221600-19223800	Enhancers	Liver	Liver
49	chr19:19221600-19229600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr19:19221600-19229600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links