Variant report

Variant	rs2304234
Chromosome Location	chr19:41748753-41748754
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41734780..41738564-chr19:41748060..41751187,3	K562	blood:
2	chr19:41748141..41750709-chr19:41755527..41757688,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10410836	0.81[ASN][1000 genomes]
rs10421990	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs11879562	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs11882467	0.94[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs12327659	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs12462203	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12975585	0.88[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap];0.85[ASN][1000 genomes]
rs12978323	0.83[ASW][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs12980480	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs12983047	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1865051	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs1865053	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs2304230	0.90[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs3745295	0.90[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs3752705	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs3786555	0.98[ASN][1000 genomes]
rs3816052	0.90[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs3826714	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4456618	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs4802111	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs4802112	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs4802113	0.89[CHB][hapmap];0.82[LWK][hapmap];0.82[ASN][1000 genomes]
rs4802115	0.99[ASN][1000 genomes]
rs4803448	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs4803449	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs4803451	0.98[ASN][1000 genomes]
rs6508974	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs66724427	0.81[ASN][1000 genomes]
rs66841352	0.88[EUR][1000 genomes]
rs6957	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7245398	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs7246525	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs7248164	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs7256416	0.81[ASN][1000 genomes]
rs7257310	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs7257825	0.81[ASN][1000 genomes]
rs7258749	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs8105161	0.87[JPT][hapmap]
rs8109167	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8109627	0.85[CHB][hapmap];0.80[CHD][hapmap];0.87[JPT][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	nsv911768	chr19:41680424-41748753	Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2304234	SLC1A5	cis	parietal	SCAN
rs2304234	ZNF226	cis	cerebellum	SCAN
rs2304234	ETHE1	cis	cerebellum	SCAN
rs2304234	BAX	cis	cerebellum	SCAN
rs2304234	FLT3LG	cis	cerebellum	SCAN
rs2304234	ZNF155	cis	parietal	SCAN
rs2304234	SIX5	cis	cerebellum	SCAN
rs2304234	PLEKHA4	cis	cerebellum	SCAN
rs2304234	PSG2	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41730200-41762600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41732600-41768800	Weak transcription	Small Intestine	intestine
3	chr19:41733200-41749400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:41733200-41767200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:41733200-41767200	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr19:41736000-41752400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr19:41736000-41767200	Strong transcription	Osteobl	bone
8	chr19:41736000-41767400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:41736200-41757000	Strong transcription	NH-A	brain
10	chr19:41736400-41767800	Strong transcription	Placenta Amnion	Placenta Amnion
11	chr19:41736600-41757200	Strong transcription	NHLF	lung
12	chr19:41736600-41766200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:41736600-41766600	Strong transcription	Fetal Stomach	stomach
14	chr19:41736600-41767000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:41736600-41767200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr19:41736600-41767400	Strong transcription	HSMM	muscle
17	chr19:41736600-41767800	Weak transcription	Brain Angular Gyrus	brain
18	chr19:41736800-41754400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr19:41736800-41758200	Strong transcription	Fetal Muscle Leg	muscle
20	chr19:41736800-41762400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:41737200-41766000	Strong transcription	Stomach Smooth Muscle	stomach
22	chr19:41737400-41766600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr19:41738000-41761000	Strong transcription	Colon Smooth Muscle	Colon
24	chr19:41738800-41767400	Weak transcription	Fetal Brain Male	brain
25	chr19:41739400-41752800	Strong transcription	NHDF-Ad	bronchial
26	chr19:41739400-41754200	Weak transcription	Left Ventricle	heart
27	chr19:41739400-41758200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr19:41739400-41767400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr19:41739600-41749600	Strong transcription	Aorta	Aorta
30	chr19:41739600-41752000	Strong transcription	Adipose Nuclei	Adipose
31	chr19:41739800-41766200	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr19:41740200-41754400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr19:41742600-41749600	Strong transcription	Rectal Smooth Muscle	rectum
34	chr19:41742600-41752200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr19:41742600-41767600	Strong transcription	A549	lung
36	chr19:41742800-41749800	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr19:41742800-41757000	Strong transcription	HSMMtube	muscle
38	chr19:41742800-41757200	Strong transcription	Ovary	ovary
39	chr19:41743000-41757000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:41743400-41752600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr19:41743400-41757200	Strong transcription	HUVEC	blood vessel
42	chr19:41743600-41749800	Strong transcription	HMEC	breast
43	chr19:41743600-41752000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:41743600-41752600	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr19:41743600-41758400	Strong transcription	Fetal Muscle Trunk	muscle
46	chr19:41743800-41761200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr19:41744200-41750800	Strong transcription	Placenta	Placenta
48	chr19:41745000-41752200	Strong transcription	Fetal Lung	lung
49	chr19:41745200-41749600	Strong transcription	Brain Anterior Caudate	brain
50	chr19:41745200-41752400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links