Variant report

Variant	rs855601
Chromosome Location	chr19:38560210-38560211
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38549096..38551828-chr19:38559673..38561442,2	MCF-7	breast:
2	chr19:38395351..38397718-chr19:38560093..38561831,2	MCF-7	breast:
3	chr19:38550744..38552362-chr19:38559660..38561600,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10412762	0.81[JPT][hapmap]
rs10413751	0.83[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10414433	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs10420506	0.81[JPT][hapmap]
rs10422665	0.81[JPT][hapmap]
rs1612361	0.82[EUR][1000 genomes]
rs1614979	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1625884	0.88[ASN][1000 genomes]
rs1654341	0.82[EUR][1000 genomes]
rs1654343	0.83[EUR][1000 genomes]
rs1654347	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1654349	0.91[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1654350	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1654352	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1654358	0.90[ASN][1000 genomes]
rs1654365	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs1725458	0.84[EUR][1000 genomes]
rs1725462	0.84[EUR][1000 genomes]
rs1725470	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1725473	0.86[ASN][1000 genomes]
rs1725475	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1725476	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1725504	0.95[TSI][hapmap]
rs1725506	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1725507	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1725508	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1725509	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1725510	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1725512	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs28412601	0.90[ASN][1000 genomes]
rs28587798	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3760882	0.88[ASN][1000 genomes]
rs3810356	0.88[ASN][1000 genomes]
rs4802233	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4802256	0.81[JPT][hapmap]
rs4803828	0.81[JPT][hapmap]
rs4803829	0.81[JPT][hapmap]
rs57585457	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57999412	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7257303	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs729626	0.94[ASN][1000 genomes]
rs855597	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855598	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs855599	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs855600	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855602	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855603	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855619	0.94[ASN][1000 genomes]
rs855624	0.94[ASN][1000 genomes]
rs855636	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs855637	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs855641	0.90[ASN][1000 genomes]
rs941040	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs9941467	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1062518	chr19:38540454-38564913	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs855601	MAP3K10	cis	parietal	SCAN
rs855601	SYMPK	cis	parietal	SCAN
rs855601	BCAM	cis	parietal	SCAN
rs855601	CCDC8	cis	parietal	SCAN
rs855601	ZNF404	cis	cerebellum	SCAN
rs855601	SNORD37	trans	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
2	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
3	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
4	chr19:38543800-38563200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr19:38546600-38572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr19:38547000-38563600	Weak transcription	Fetal Lung	lung
7	chr19:38547200-38561400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:38549200-38564800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr19:38549200-38572000	Weak transcription	Liver	Liver
10	chr19:38549600-38572600	Weak transcription	Thymus	Thymus
11	chr19:38550000-38561000	Weak transcription	Hela-S3	cervix
12	chr19:38550000-38570400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr19:38550800-38563400	Weak transcription	Spleen	Spleen
14	chr19:38550800-38565200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr19:38550800-38570000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr19:38550800-38572200	Weak transcription	Colonic Mucosa	Colon
17	chr19:38550800-38590000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr19:38551000-38572000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr19:38551200-38562200	Weak transcription	Primary T cells from cord blood	blood
20	chr19:38551200-38562600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr19:38551200-38563600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr19:38551200-38567000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr19:38551400-38562400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:38551400-38567000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:38552400-38560800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:38552400-38561000	Weak transcription	NHEK	skin
28	chr19:38552400-38561200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:38553200-38570400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:38553800-38561200	Weak transcription	NH-A	brain
31	chr19:38553800-38561400	Weak transcription	Esophagus	oesophagus
32	chr19:38553800-38561400	Weak transcription	Lung	lung
33	chr19:38553800-38572000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:38554200-38561400	Weak transcription	Pancreas	Pancrea
35	chr19:38554200-38572600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr19:38554400-38561000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:38554400-38564600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:38554600-38561000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:38554600-38567000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr19:38554600-38570400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:38554600-38571800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:38554800-38561400	Weak transcription	HSMM	muscle
43	chr19:38554800-38562000	Strong transcription	Fetal Intestine Small	intestine
44	chr19:38554800-38563600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr19:38554800-38571800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr19:38554800-38573200	Weak transcription	Brain Angular Gyrus	brain
47	chr19:38554800-38580200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr19:38555000-38562000	Weak transcription	Fetal Stomach	stomach
49	chr19:38555000-38563400	Weak transcription	Fetal Muscle Leg	muscle
50	chr19:38555000-38570800	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links