Variant report

Variant	rs2815406
Chromosome Location	chr1:93629673-93629674
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	chr1:93629615..93631594-chr1:93632209..93633855,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1010476	0.94[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10874766	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11164876	0.81[ASN][1000 genomes]
rs11164908	0.85[CHB][hapmap]
rs12027142	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12030843	0.85[CHB][hapmap]
rs12033147	0.88[CHB][hapmap]
rs12038046	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12044557	0.89[CHB][hapmap]
rs12046063	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12563120	0.89[CHB][hapmap]
rs2255722	0.94[CHB][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2281524	0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2281525	0.85[CHB][hapmap]
rs2484486	0.94[CHB][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2749732	0.88[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2783489	0.81[ASN][1000 genomes]
rs2783490	0.94[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2783493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783495	0.94[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2783496	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2783497	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2783499	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs2783500	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs2783501	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs2783504	0.80[ASN][1000 genomes]
rs2783505	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2815415	0.82[ASN][1000 genomes]
rs2815429	0.88[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28782525	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2893242	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3904666	0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4484937	0.89[CHB][hapmap]
rs4847235	0.81[ASN][1000 genomes]
rs489183	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs556446	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs579138	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61799470	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61799496	0.80[ASN][1000 genomes]
rs61799497	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6541349	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS 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	34 gene(s)	inside rSNPs	diseases
3	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2815406	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs2815406	CCDC18	cis	multi-tissue	Pritchard

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93574600-93630200	Weak transcription	Right Ventricle	heart
2	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:93582400-93642800	Weak transcription	Gastric	stomach
4	chr1:93583600-93635400	Weak transcription	Pancreas	Pancrea
5	chr1:93585800-93642200	Weak transcription	Esophagus	oesophagus
6	chr1:93595800-93635600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:93600400-93635400	Weak transcription	Spleen	Spleen
8	chr1:93601000-93643600	Weak transcription	HSMMtube	muscle
9	chr1:93601400-93635400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:93602600-93630200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:93602600-93630200	Weak transcription	Brain Anterior Caudate	brain
12	chr1:93606000-93644600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:93606800-93635400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:93611800-93644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:93614200-93630200	Weak transcription	Right Atrium	heart
16	chr1:93614200-93634800	Weak transcription	A549	lung
17	chr1:93615200-93630200	Weak transcription	Psoas Muscle	Psoas
18	chr1:93615600-93643200	Weak transcription	Fetal Kidney	kidney
19	chr1:93618200-93630800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:93618600-93630200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:93620800-93635600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:93621400-93630200	Weak transcription	Small Intestine	intestine
23	chr1:93621400-93632000	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:93621400-93632200	Weak transcription	Fetal Stomach	stomach
25	chr1:93621400-93635400	Weak transcription	Thymus	Thymus
26	chr1:93621400-93635600	Weak transcription	Lung	lung
27	chr1:93621400-93636800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:93621400-93637800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:93621400-93640000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:93621400-93643000	Weak transcription	HMEC	breast
31	chr1:93621400-93643800	Weak transcription	Colonic Mucosa	Colon
32	chr1:93621600-93641400	Weak transcription	NHEK	skin
33	chr1:93622200-93631400	Weak transcription	Fetal Brain Female	brain
34	chr1:93622200-93637200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:93622400-93636400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:93623200-93633200	Weak transcription	Hela-S3	cervix
37	chr1:93624000-93637200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:93624000-93643400	Weak transcription	NH-A	brain
39	chr1:93624000-93643600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr1:93624200-93636400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:93624400-93643600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:93624800-93636400	Weak transcription	Primary T cells from cord blood	blood
43	chr1:93624800-93641600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:93624800-93643600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:93624800-93643600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:93625000-93630200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:93625000-93630600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:93625000-93631000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:93625000-93636600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:93625000-93640000	Weak transcription	K562	blood

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