Variant report

Variant	rs35769610
Chromosome Location	chr21:40677046-40677047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40671195..40673748-chr21:40675125..40678603,4	K562	blood:
2	chr21:40675820..40678831-chr21:40721085..40724268,3	K562	blood:
3	chr21:40675223..40677979-chr21:40720098..40723094,2	MCF-7	breast:
4	chr21:40671338..40675047-chr21:40676117..40679838,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WRB-5	chr21:40676880-40677252	ucscGeneNc_uc002yyu_2

Variant related genes	Relation type
ENSG00000205581	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1029004	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10854396	0.86[ASN][1000 genomes]
rs11088466	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11088470	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11701805	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11702505	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11910232	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11911087	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12483559	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12627205	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13047518	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13049907	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1474490	0.83[EUR][1000 genomes]
rs1980407	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2056844	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2070865	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2150411	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2150413	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2150414	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2297256	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836926	0.84[EUR][1000 genomes]
rs2836930	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836931	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2836934	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2836940	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2836942	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836943	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836945	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836948	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836949	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836952	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836956	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836958	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836959	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836966	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836980	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836983	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836984	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836985	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3171465	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34705151	0.83[EUR][1000 genomes]
rs34890172	0.84[EUR][1000 genomes]
rs35994303	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4816617	0.85[EUR][1000 genomes]
rs4816618	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4818001	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4818015	0.81[AFR][1000 genomes]
rs4818018	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4818019	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59916147	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61300849	0.80[AFR][1000 genomes]
rs62223011	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62223039	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62223052	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7276046	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7278297	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7279497	0.85[EUR][1000 genomes]
rs7282582	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8127379	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8129595	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8130162	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8130240	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8130320	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8131132	0.85[EUR][1000 genomes]
rs8132143	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8132424	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8133928	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8134214	0.85[EUR][1000 genomes]
rs8134843	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459259	chr21:40571246-40701169	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv587480	chr21:40571246-40701169	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3429298	chr21:40670131-40688774	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35769610	BRWD1	Cis_1M	lymphoblastoid	RTeQTL
rs35769610	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs35769610	PSMG1	cis	Artery Tibial	GTEx
rs35769610	HMGN1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40641400-40683800	Strong transcription	Placenta	Placenta
2	chr21:40643800-40684200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr21:40646600-40683400	Weak transcription	Fetal Brain Male	brain
4	chr21:40655000-40683000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr21:40655400-40683200	Strong transcription	Dnd41	blood
6	chr21:40655800-40677400	Strong transcription	Duodenum Mucosa	Duodenum
7	chr21:40655800-40677400	Strong transcription	Fetal Thymus	thymus
8	chr21:40656400-40683800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr21:40661800-40683400	Weak transcription	Stomach Mucosa	stomach
10	chr21:40663600-40683400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr21:40664000-40684200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr21:40665000-40683800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr21:40665200-40684400	Weak transcription	Colonic Mucosa	Colon
14	chr21:40666000-40682600	Weak transcription	NHLF	lung
15	chr21:40667000-40684000	Weak transcription	HSMMtube	muscle
16	chr21:40667000-40684200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr21:40669200-40684200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr21:40669400-40684000	Weak transcription	HUVEC	blood vessel
19	chr21:40669400-40684400	Weak transcription	Esophagus	oesophagus
20	chr21:40669800-40679800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr21:40669800-40683800	Weak transcription	Brain Substantia Nigra	brain
22	chr21:40670400-40677200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr21:40670400-40677400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr21:40670400-40680600	Weak transcription	Brain Hippocampus Middle	brain
25	chr21:40670400-40683800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr21:40670600-40683200	Weak transcription	NHDF-Ad	bronchial
27	chr21:40670800-40679600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr21:40670800-40679800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr21:40670800-40680000	Weak transcription	HepG2	liver
30	chr21:40671400-40683200	Weak transcription	HMEC	breast
31	chr21:40672200-40684000	Weak transcription	Aorta	Aorta
32	chr21:40672400-40683400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr21:40672400-40684000	Weak transcription	Small Intestine	intestine
34	chr21:40672600-40677200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr21:40672600-40679600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr21:40672600-40682400	Weak transcription	Brain Anterior Caudate	brain
37	chr21:40672600-40682600	Weak transcription	Psoas Muscle	Psoas
38	chr21:40672600-40683800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr21:40672600-40684400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr21:40672800-40679800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr21:40672800-40683400	Weak transcription	Fetal Heart	heart
42	chr21:40672800-40683800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr21:40673200-40677200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr21:40673200-40677600	Strong transcription	Liver	Liver
45	chr21:40673600-40677200	Strong transcription	Fetal Stomach	stomach
46	chr21:40673600-40678000	Strong transcription	Fetal Intestine Small	intestine
47	chr21:40673600-40679600	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr21:40673600-40679800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr21:40673600-40680800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr21:40673600-40682400	Weak transcription	H9 Cell Line	embryonic stem cell

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