Variant report

Variant	rs8104799
Chromosome Location	chr19:19151692-19151693
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19143762..19145287-chr19:19149753..19152112,2	K562	blood:
2	chr19:19150556..19153646-chr19:19160742..19164221,4	K562	blood:
3	chr19:19142730..19148953-chr19:19149447..19156213,13	K562	blood:
4	chr19:19151085..19153455-chr19:19230686..19233171,2	K562	blood:

Variant related genes	Relation type
ENSG00000105676	Chromatin interaction
ENSG00000064545	Chromatin interaction
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1007483	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10221504	0.95[ASN][1000 genomes]
rs10403222	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10403322	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10404627	0.95[ASN][1000 genomes]
rs10405189	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405635	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs10409164	0.95[ASN][1000 genomes]
rs10410451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10410568	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10414676	0.82[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10416783	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417974	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10422335	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10422906	0.95[ASN][1000 genomes]
rs10423742	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs10423815	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079543	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10854005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1124921	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666120	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11666340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11670204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670239	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11878368	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12016	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12975676	0.95[ASN][1000 genomes]
rs12975754	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12976302	0.92[ASN][1000 genomes]
rs12978822	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12979565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12985799	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1859267	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012318	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2107263	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2158320	1.00[ASN][1000 genomes]
rs2240094	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240095	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269806	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2269869	0.84[CEU][hapmap]
rs2285851	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2313736	0.97[ASN][1000 genomes]
rs2872394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3180770	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808172	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs4808179	1.00[ASN][1000 genomes]
rs4808184	0.95[ASN][1000 genomes]
rs4808900	0.89[AFR][1000 genomes]
rs4808902	0.97[ASN][1000 genomes]
rs4808904	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808905	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808906	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808907	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808911	1.00[ASN][1000 genomes]
rs4808913	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808916	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs6511010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6511011	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6511014	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6511015	1.00[ASN][1000 genomes]
rs6511017	1.00[ASN][1000 genomes]
rs6511018	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6511021	0.82[CEU][hapmap];0.85[CHB][hapmap]
rs7248399	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7248771	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7250131	0.95[ASN][1000 genomes]
rs7253244	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7255937	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7257635	0.91[ASN][1000 genomes]
rs7258637	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259510	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259609	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs757220	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8101529	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8103431	0.95[ASN][1000 genomes]
rs8104754	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8106146	0.86[CHB][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107710	0.90[ASN][1000 genomes]
rs8109654	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111634	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111635	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8112566	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs916898	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs929215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304959	1.00[ASN][1000 genomes]
rs9676917	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv1059305	chr19:19131310-19209999	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
3	nsv543927	chr19:19147376-19178024	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs8104799	KIAA1683	cis	cerebellum	SCAN
rs8104799	NDUFA13	cis	parietal	SCAN
rs8104799	MED26	cis	cerebellum	SCAN
rs8104799	ZNF506	cis	parietal	SCAN
rs8104799	TMEM161A	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19145000-19154800	Weak transcription	Aorta	Aorta
2	chr19:19145000-19174000	Weak transcription	Small Intestine	intestine
3	chr19:19145200-19153600	Weak transcription	Ovary	ovary
4	chr19:19145400-19153400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr19:19145400-19165600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr19:19145400-19171800	Weak transcription	Right Atrium	heart
7	chr19:19145600-19153200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr19:19145600-19153400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:19145600-19153400	Weak transcription	Brain Substantia Nigra	brain
10	chr19:19145600-19153400	Weak transcription	Colonic Mucosa	Colon
11	chr19:19145600-19153400	Weak transcription	Gastric	stomach
12	chr19:19145600-19153400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr19:19145600-19153600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr19:19145600-19153600	Weak transcription	Brain Anterior Caudate	brain
15	chr19:19145600-19153600	Weak transcription	Brain Hippocampus Middle	brain
16	chr19:19145600-19153600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr19:19145600-19153600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr19:19145600-19153800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr19:19145600-19154000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr19:19145600-19154600	Weak transcription	HUVEC	blood vessel
21	chr19:19145600-19154600	Weak transcription	NHDF-Ad	bronchial
22	chr19:19145600-19154800	Weak transcription	Brain Angular Gyrus	brain
23	chr19:19145600-19154800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr19:19145600-19159600	Weak transcription	NH-A	brain
25	chr19:19145600-19172200	Weak transcription	Stomach Mucosa	stomach
26	chr19:19145600-19173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:19145600-19173800	Weak transcription	Fetal Kidney	kidney
28	chr19:19145800-19153400	Weak transcription	Spleen	Spleen
29	chr19:19146200-19153600	Weak transcription	Right Ventricle	heart
30	chr19:19146200-19154000	Weak transcription	Left Ventricle	heart
31	chr19:19146400-19153400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:19146400-19153600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:19146600-19161800	Weak transcription	Psoas Muscle	Psoas
34	chr19:19146800-19153400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr19:19147400-19153400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr19:19148400-19161600	Weak transcription	Fetal Heart	heart
37	chr19:19148800-19153400	Weak transcription	Esophagus	oesophagus
38	chr19:19148800-19153400	Weak transcription	Fetal Intestine Large	intestine
39	chr19:19148800-19153400	Weak transcription	Placenta	Placenta
40	chr19:19148800-19153600	Weak transcription	HMEC	breast
41	chr19:19148800-19153800	Weak transcription	NHEK	skin
42	chr19:19149000-19151800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:19149000-19153200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:19149000-19153200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:19149000-19153400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr19:19149000-19153400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:19149000-19153400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr19:19149000-19153400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:19149000-19153400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr19:19149000-19154000	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links