Variant report

Variant	rs378825
Chromosome Location	chr11:9766932-9766933
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	chr11:9759666..9763532-chr11:9766394..9768623,4	K562	blood:
2	chr11:9759666..9763371-chr11:9766657..9768623,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WEE1-3	chr11:9766574-9768012	NONHSAT017934

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1032550	0.94[JPT][hapmap]
rs10743117	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10743118	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10840293	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10840294	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10840295	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10840296	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840305	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs10840306	0.90[JPT][hapmap]
rs12360647	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12788348	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs173396	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1996794	0.89[JPT][hapmap]
rs2649044	0.86[AMR][1000 genomes]
rs360136	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs360137	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs360139	0.89[ASN][1000 genomes]
rs360153	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs360155	0.88[EUR][1000 genomes]
rs360156	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs360157	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360158	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs373894	0.94[ASN][1000 genomes]
rs3751000	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs415895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs429835	0.83[JPT][hapmap]
rs472109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4910063	0.95[JPT][hapmap]
rs4910498	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4910499	0.96[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs491205	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7126913	0.92[JPT][hapmap]
rs93138	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs93139	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9943599	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1045550	chr11:9718324-9790088	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv527910	chr11:9765348-9769063	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9742200-9779400	Weak transcription	Fetal Brain Male	brain
2	chr11:9745000-9775600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:9755000-9777600	Weak transcription	Colonic Mucosa	Colon
4	chr11:9755400-9769800	Weak transcription	Pancreas	Pancrea
5	chr11:9757400-9769200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr11:9757600-9774600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:9758400-9769800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr11:9758400-9769800	Weak transcription	Stomach Mucosa	stomach
9	chr11:9758800-9769800	Weak transcription	Brain Anterior Caudate	brain
10	chr11:9758800-9776000	Weak transcription	Brain Germinal Matrix	brain
11	chr11:9759200-9769400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:9760600-9769800	Weak transcription	Fetal Heart	heart
13	chr11:9761000-9769400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:9761000-9777200	Weak transcription	Fetal Kidney	kidney
15	chr11:9761800-9772200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr11:9762200-9769400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:9762200-9769400	Weak transcription	Ovary	ovary
18	chr11:9762200-9771600	Weak transcription	Aorta	Aorta
19	chr11:9762400-9767200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:9762400-9769200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr11:9762400-9769800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr11:9762400-9772000	Weak transcription	Gastric	stomach
23	chr11:9762400-9777200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr11:9762400-9777400	Weak transcription	Esophagus	oesophagus
25	chr11:9762400-9777400	Weak transcription	Right Ventricle	heart
26	chr11:9762400-9779400	Weak transcription	Liver	Liver
27	chr11:9762400-9779400	Weak transcription	Psoas Muscle	Psoas
28	chr11:9762600-9767200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr11:9762600-9769000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:9762600-9769200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr11:9762600-9769800	Weak transcription	Brain Angular Gyrus	brain
32	chr11:9762600-9769800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr11:9762600-9769800	Weak transcription	Brain Hippocampus Middle	brain
34	chr11:9762600-9779200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr11:9762800-9769800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr11:9762800-9779400	Weak transcription	Fetal Brain Female	brain
37	chr11:9763000-9769800	Weak transcription	Brain Substantia Nigra	brain
38	chr11:9763000-9770000	Weak transcription	Small Intestine	intestine
39	chr11:9763200-9767400	Weak transcription	Fetal Thymus	thymus
40	chr11:9763200-9768800	Weak transcription	Hela-S3	cervix
41	chr11:9763200-9769400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr11:9763200-9773600	Weak transcription	HepG2	liver
43	chr11:9763200-9775200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:9763400-9769200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr11:9763400-9769400	Weak transcription	Colon Smooth Muscle	Colon
46	chr11:9763600-9772000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr11:9763600-9779400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr11:9763800-9769800	Weak transcription	Primary T cells from cord blood	blood
49	chr11:9763800-9769800	Weak transcription	Osteobl	bone
50	chr11:9763800-9770000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links