Variant report

Variant	rs2484486
Chromosome Location	chr1:93651500-93651501
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	chr1:93650348..93652669-chr1:93667602..93669955,2	K562	blood:

Extended variants
information (count: 105 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1010476	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1060622	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs10782959	0.95[CHD][hapmap];0.80[GIH][hapmap]
rs10874766	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11164870	0.81[CHB][hapmap]
rs11164876	0.85[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs11164879	0.81[CHB][hapmap]
rs11164880	0.80[ASN][1000 genomes]
rs11164896	0.88[EUR][1000 genomes]
rs11164905	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs11164908	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs12027142	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12030549	0.81[CHB][hapmap]
rs12030843	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs12033147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs12036057	0.80[EUR][1000 genomes]
rs12038046	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12038699	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs12044557	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs12044883	0.88[CHB][hapmap]
rs12045001	0.88[EUR][1000 genomes]
rs12046063	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12118262	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs12128131	0.89[CHB][hapmap]
rs12133576	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs12563120	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs12563709	0.88[EUR][1000 genomes]
rs1335679	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs1426318	0.81[CHB][hapmap]
rs1474927	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs1537758	0.80[ASN][1000 genomes]
rs1559828	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs1572343	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs1856027	0.82[CHD][hapmap]
rs2031225	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs2255722	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2281524	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2281525	0.89[CHB][hapmap]
rs2295423	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs2296558	0.81[CHB][hapmap]
rs2391254	0.81[CHB][hapmap]
rs2749732	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs2765545	0.89[CHD][hapmap]
rs2783489	0.85[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs2783490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2783493	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2783495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2783496	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2783497	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2783499	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs2783500	1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs2783501	0.95[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs2783504	0.86[ASN][1000 genomes]
rs2783505	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2815406	0.94[CHB][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2815415	0.87[ASN][1000 genomes]
rs2815429	0.95[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs28782525	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2893242	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3087457	0.80[EUR][1000 genomes]
rs3754186	0.81[CHB][hapmap]
rs3767964	0.81[CHB][hapmap]
rs3904665	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs3904666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4000699	0.81[CHB][hapmap]
rs4240966	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs4484937	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs4847235	0.85[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs4847240	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs4847399	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs4847408	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs489183	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs531358	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs556446	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs579138	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs612037	0.81[CHB][hapmap]
rs61799470	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61799496	0.86[ASN][1000 genomes]
rs61799497	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61799517	0.88[EUR][1000 genomes]
rs622608	0.81[CHB][hapmap]
rs6541349	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs6541401	0.81[CHB][hapmap]
rs6541404	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs6682670	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs6703310	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs693737	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs7513705	0.85[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs7517363	0.80[CHB][hapmap];0.87[CHD][hapmap]
rs7525248	0.85[CHB][hapmap]
rs7535628	0.85[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7539307	0.85[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs771454	0.80[EUR][1000 genomes]
rs771461	0.80[EUR][1000 genomes]
rs771465	0.80[EUR][1000 genomes]
rs771476	0.80[EUR][1000 genomes]
rs771479	0.80[EUR][1000 genomes]
rs771481	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs771482	0.80[EUR][1000 genomes]
rs797668	0.81[CHB][hapmap]
rs797680	0.81[CHB][hapmap]
rs810027	0.80[EUR][1000 genomes]
rs942196	0.81[CHB][hapmap]

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	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
2	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2484486	DR1	cis	parietal	SCAN
rs2484486	LRRC8D	cis	parietal	SCAN
rs2484486	GLMN	cis	cerebellum	SCAN
rs2484486	CCDC18	cis	parietal	SCAN
rs2484486	CCDC18	cis	multi-tissue	Pritchard

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93646600-93660400	Weak transcription	Lung	lung
2	chr1:93646800-93664600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:93647000-93663600	Weak transcription	Fetal Stomach	stomach
4	chr1:93647000-93664600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:93647000-93688000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:93647000-93688600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:93647000-93756400	Weak transcription	Gastric	stomach
8	chr1:93647200-93651600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:93647200-93652400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:93647200-93654200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:93647200-93657600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:93647200-93658000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:93647200-93660400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:93647200-93660400	Weak transcription	Thymus	Thymus
15	chr1:93647200-93660800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:93647200-93661400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:93647200-93664200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:93647200-93664200	Weak transcription	Fetal Intestine Small	intestine
19	chr1:93647200-93664400	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:93647200-93664600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:93647200-93664600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:93647200-93667600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:93647200-93667600	Weak transcription	Adipose Nuclei	Adipose
24	chr1:93647200-93668200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:93647200-93681200	Weak transcription	HUVEC	blood vessel
26	chr1:93647200-93684400	Weak transcription	NH-A	brain
27	chr1:93647200-93685000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:93647200-93707400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:93647400-93659000	Weak transcription	HSMM	muscle
31	chr1:93647400-93661000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:93647400-93664800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:93647400-93667400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:93647600-93652000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:93647600-93654400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:93647600-93657600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:93647600-93657800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:93647600-93660400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:93647600-93664400	Weak transcription	NHLF	lung
40	chr1:93647600-93670400	Weak transcription	Liver	Liver
41	chr1:93647600-93706600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:93647800-93660400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:93647800-93665000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:93647800-93667800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:93648000-93651600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr1:93648000-93651600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr1:93648000-93652400	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr1:93648000-93654600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:93648000-93657600	Weak transcription	Osteobl	bone
50	chr1:93648000-93658000	Weak transcription	Primary T cells from cord blood	blood

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