Variant report

Variant	rs444816
Chromosome Location	chr19:44438366-44438367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44330249..44332710-chr19:44437495..44440338,2	MCF-7	breast:
2	chr19:44435828..44438682-chr19:44451938..44454086,2	K562	blood:
3	chr19:44330466..44332260-chr19:44438054..44440025,2	K562	blood:

Variant related genes	Relation type
ENSG00000167637	Chromatin interaction
ENSG00000159871	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10402944	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2299936	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2429734	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs364278	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs366431	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs368492	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs376655	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs377931	0.96[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs377934	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs381220	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381872	0.92[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs385202	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386249	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386747	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs387504	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs388547	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs390134	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs391961	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394132	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs394380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs395419	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs396188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397276	0.85[CEU][hapmap]
rs400591	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413061	0.92[CEU][hapmap];0.80[CHB][hapmap];0.92[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs415468	0.84[EUR][1000 genomes]
rs415867	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418336	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs424041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427401	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs429611	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs437700	0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs441386	0.92[CEU][hapmap];0.80[CHB][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs441742	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442543	0.83[AMR][1000 genomes]
rs445865	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs453682	1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs454376	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv579854	chr19:44411543-44490024	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs444816	CYTH2	cis	parietal	SCAN
rs444816	VSIG10L	cis	parietal	SCAN
rs444816	KLC3	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44419400-44438600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:44420400-44438600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:44424000-44438600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:44434400-44438600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:44434800-44438400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:44434800-44438400	Weak transcription	Pancreas	Pancrea
7	chr19:44434800-44438400	Weak transcription	Right Ventricle	heart
8	chr19:44434800-44438400	Weak transcription	Spleen	Spleen
9	chr19:44435600-44438600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:44436200-44438600	Weak transcription	Esophagus	oesophagus
11	chr19:44436400-44438600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr19:44436800-44438400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:44437000-44438600	Weak transcription	Aorta	Aorta
14	chr19:44437200-44438400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr19:44437200-44438400	Weak transcription	Placenta	Placenta
16	chr19:44437200-44438400	Weak transcription	Gastric	stomach
17	chr19:44437200-44438600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr19:44437400-44438400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:44437400-44438400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr19:44437400-44438400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:44437400-44438400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:44437400-44438400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr19:44437400-44438600	Weak transcription	Left Ventricle	heart
24	chr19:44437600-44438400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr19:44437600-44438400	Enhancers	Colon Smooth Muscle	Colon
26	chr19:44437600-44438400	Weak transcription	Lung	lung
27	chr19:44437600-44438400	Weak transcription	Ovary	ovary
28	chr19:44437800-44438800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:44438000-44438400	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr19:44438000-44438400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr19:44438000-44438400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr19:44438000-44438400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr19:44438000-44438400	Enhancers	Fetal Intestine Small	intestine
34	chr19:44438000-44438400	Enhancers	Fetal Muscle Leg	muscle
35	chr19:44438000-44438400	Enhancers	Fetal Stomach	stomach
36	chr19:44438000-44438400	Enhancers	Fetal Thymus	thymus
37	chr19:44438000-44438600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr19:44438000-44438600	Enhancers	Primary B cells from peripheral blood	blood
39	chr19:44438000-44438800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:44438000-44438800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:44438000-44438800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr19:44438000-44438800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:44438000-44438800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr19:44438000-44438800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:44438000-44438800	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr19:44438000-44438800	Flanking Active TSS	Dnd41	blood
47	chr19:44438000-44439000	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr19:44438000-44439000	Flanking Active TSS	HUVEC	blood vessel
49	chr19:44438000-44439200	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr19:44438000-44439200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links