Variant report

Variant	rs16975663
Chromosome Location	chr19:42593716-42593717
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:42592734..42594940-chr19:42596414..42600451,3	K562	blood:
2	chr19:42552423..42554392-chr19:42592510..42594306,2	K562	blood:
3	chr19:42588900..42591593-chr19:42593141..42596023,2	K562	blood:
4	chr19:42579277..42583219-chr19:42593015..42597693,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000028277	Chromatin interaction
ENSG00000105732	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10407506	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10500285	0.93[CHD][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs11878620	0.94[LWK][hapmap];1.00[YRI][hapmap]
rs11878917	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11880124	0.85[CHD][hapmap];0.83[GIH][hapmap];0.94[LWK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs11883412	0.83[ASW][hapmap];0.90[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap]
rs16975684	0.80[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap]
rs17270169	0.90[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs17342067	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17342284	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs2303652	0.83[ASW][hapmap];0.90[CEU][hapmap];0.83[GIH][hapmap];0.94[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs3736109	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs3745231	0.90[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap]
rs3745233	0.83[ASW][hapmap];0.90[CEU][hapmap];0.83[GIH][hapmap];0.94[LWK][hapmap];0.94[YRI][hapmap]
rs3810151	0.80[CEU][hapmap]
rs3826705	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs407096	0.89[AFR][1000 genomes]
rs443239	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs454150	1.00[ASW][hapmap];0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes]
rs4803520	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs61195828	0.85[ASN][1000 genomes]
rs7248379	0.80[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap]
rs7251466	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.85[ASN][1000 genomes]
rs7253767	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7253791	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7253915	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8106871	0.80[ASN][1000 genomes]
rs8107107	0.83[ASW][hapmap];0.89[LWK][hapmap];0.82[YRI][hapmap]
rs8182491	0.80[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap]
rs899661	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv911783	chr19:42575462-42624662	Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42582200-42596000	Weak transcription	Right Atrium	heart
2	chr19:42582200-42597800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:42582400-42594000	Weak transcription	Fetal Brain Male	brain
4	chr19:42582400-42594800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:42582400-42595600	Weak transcription	Fetal Heart	heart
6	chr19:42582400-42595800	Weak transcription	Hela-S3	cervix
7	chr19:42582400-42597800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr19:42585800-42595600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr19:42585800-42595800	Weak transcription	Small Intestine	intestine
10	chr19:42586000-42594000	Weak transcription	Colonic Mucosa	Colon
11	chr19:42586000-42594800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr19:42586000-42595600	Weak transcription	Gastric	stomach
13	chr19:42586000-42595800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:42586000-42598800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr19:42586000-42601600	Weak transcription	Pancreas	Pancrea
16	chr19:42586000-42606400	Weak transcription	Liver	Liver
17	chr19:42586200-42595400	Weak transcription	Esophagus	oesophagus
18	chr19:42586200-42595400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr19:42586200-42598400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr19:42586200-42600400	Weak transcription	Brain Substantia Nigra	brain
21	chr19:42586400-42596000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:42586400-42596200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:42586400-42597800	Weak transcription	Primary T cells from cord blood	blood
24	chr19:42586600-42594000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr19:42586600-42595600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:42586600-42595800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr19:42586600-42595800	Weak transcription	K562	blood
28	chr19:42586600-42596000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr19:42586600-42596000	Weak transcription	Right Ventricle	heart
30	chr19:42586600-42597400	Weak transcription	Brain Germinal Matrix	brain
31	chr19:42586600-42598400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr19:42586600-42599800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:42586600-42626600	Weak transcription	Brain Anterior Caudate	brain
34	chr19:42586600-42627600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:42586600-42631600	Weak transcription	Brain Angular Gyrus	brain
36	chr19:42586800-42596400	Weak transcription	Dnd41	blood
37	chr19:42587000-42598000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:42588400-42595800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr19:42588800-42594600	Weak transcription	Fetal Brain Female	brain
40	chr19:42588800-42596400	Weak transcription	Thymus	Thymus
41	chr19:42590000-42595200	Enhancers	Primary B cells from peripheral blood	blood
42	chr19:42590400-42593800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:42591800-42594600	Enhancers	GM12878-XiMat	blood
44	chr19:42591800-42594800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:42592200-42597800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:42592400-42593800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr19:42592600-42594400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:42592800-42593800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:42592800-42593800	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr19:42592800-42594400	Enhancers	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links