Variant report

Variant	rs7341998
Chromosome Location	chr10:99284457-99284458
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	chr10:99271315..99274212-chr10:99282293..99285243,2	K562	blood:
2	chr10:99278192..99281004-chr10:99284168..99285856,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10786353	0.88[CHB][hapmap];0.81[ASN][1000 genomes]
rs10882949	0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs10882953	0.82[CEU][hapmap]
rs11189249	0.86[CHD][hapmap]
rs11189257	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189258	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11592144	0.82[CEU][hapmap];0.93[GIH][hapmap];0.83[TSI][hapmap]
rs1890969	0.81[ASN][1000 genomes]
rs7074482	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1036494	chr10:99267639-99345207	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7341998	CC2D2B	cis	cerebellum	SCAN
rs7341998	FRAT2	cis	cerebellum	SCAN
rs7341998	LOXL4	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99270800-99286200	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr10:99274200-99285000	Enhancers	Right Ventricle	heart
3	chr10:99275000-99293800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr10:99277800-99301800	Weak transcription	Gastric	stomach
5	chr10:99278000-99302600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr10:99278200-99298800	Weak transcription	Aorta	Aorta
7	chr10:99278400-99289600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr10:99278400-99301800	Weak transcription	Spleen	Spleen
9	chr10:99278600-99300200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr10:99279400-99284600	Weak transcription	Adipose Nuclei	Adipose
11	chr10:99279800-99284600	Weak transcription	Brain Angular Gyrus	brain
12	chr10:99279800-99287200	Enhancers	Lung	lung
13	chr10:99280200-99284600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr10:99281200-99291400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr10:99281400-99302200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr10:99282200-99289400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr10:99282200-99289600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr10:99282200-99301800	Weak transcription	Pancreas	Pancrea
19	chr10:99282400-99291200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr10:99282400-99298200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr10:99282800-99292800	Weak transcription	HSMMtube	muscle
22	chr10:99282800-99299400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr10:99283000-99284600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr10:99283800-99285200	Enhancers	Brain Hippocampus Middle	brain
25	chr10:99284000-99284600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr10:99284000-99284600	Weak transcription	Psoas Muscle	Psoas
27	chr10:99284200-99284800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr10:99284400-99284800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr10:99284400-99284800	Enhancers	Brain Anterior Caudate	brain
30	chr10:99284400-99284800	Enhancers	Brain Cingulate Gyrus	brain
31	chr10:99284400-99284800	Enhancers	Esophagus	oesophagus
32	chr10:99284400-99284800	Enhancers	Fetal Muscle Trunk	muscle
33	chr10:99284400-99284800	Enhancers	Ovary	ovary
34	chr10:99284400-99285000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr10:99284400-99285000	Enhancers	Brain Substantia Nigra	brain
36	chr10:99284400-99285000	Enhancers	Left Ventricle	heart
37	chr10:99284400-99285200	Enhancers	Right Atrium	heart
38	chr10:99284400-99285400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr10:99284400-99287600	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links