Variant report

Variant	rs3800499
Chromosome Location	chr6:12120090-12120091
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:12119694..12121745-chr6:12128409..12130383,2	MCF-7	breast:
2	chr6:12101827..12103669-chr6:12119606..12121649,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10947756	0.81[GIH][hapmap]
rs12662314	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12663812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12664121	0.82[AMR][1000 genomes]
rs12664849	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16872348	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2157492	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2157494	0.90[MEX][hapmap]
rs2228211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2327512	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28769650	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777756	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3777757	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777767	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3777777	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4317394	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4443504	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4484521	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4714187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55637995	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6910367	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6917623	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6931770	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72828103	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72828104	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72828110	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7449638	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7741589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7747677	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9380769	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870443	chr6:12096356-12125998	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3800499	JARID2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12070800-12120400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:12071800-12120400	Weak transcription	HepG2	liver
3	chr6:12091000-12130600	Weak transcription	Psoas Muscle	Psoas
4	chr6:12103800-12120400	Weak transcription	Small Intestine	intestine
5	chr6:12106000-12120600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:12106000-12120600	Weak transcription	Esophagus	oesophagus
7	chr6:12106200-12120400	Weak transcription	Fetal Kidney	kidney
8	chr6:12106800-12120400	Weak transcription	Gastric	stomach
9	chr6:12107400-12120400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:12107400-12124800	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:12107600-12120800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:12107800-12120600	Weak transcription	Brain Angular Gyrus	brain
13	chr6:12108200-12120200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:12108400-12120400	Weak transcription	Colonic Mucosa	Colon
15	chr6:12108600-12120200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:12108600-12120400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr6:12110200-12120400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:12110800-12120400	Weak transcription	Hela-S3	cervix
19	chr6:12111200-12120400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:12111400-12120400	Weak transcription	Fetal Brain Male	brain
21	chr6:12112000-12120200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:12112000-12120400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:12112000-12120400	Weak transcription	Fetal Lung	lung
24	chr6:12112200-12120200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr6:12113200-12120200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:12113200-12120400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:12113400-12120400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:12113400-12120400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:12113400-12120600	Weak transcription	Placenta	Placenta
30	chr6:12113600-12120200	Weak transcription	Lung	lung
31	chr6:12113600-12120400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:12113600-12120400	Weak transcription	Spleen	Spleen
33	chr6:12113800-12121400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:12114000-12120200	Weak transcription	HUVEC	blood vessel
35	chr6:12114000-12120400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:12114000-12120400	Weak transcription	HMEC	breast
37	chr6:12114000-12120400	Weak transcription	NHEK	skin
38	chr6:12114000-12120400	Weak transcription	NHLF	lung
39	chr6:12114200-12120200	Weak transcription	K562	blood
40	chr6:12114200-12120400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:12114200-12120400	Weak transcription	HSMM	muscle
42	chr6:12114200-12120800	Weak transcription	NHDF-Ad	bronchial
43	chr6:12114200-12121000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr6:12114400-12120200	Weak transcription	NH-A	brain
45	chr6:12114400-12120800	Weak transcription	Osteobl	bone
46	chr6:12114800-12120200	Weak transcription	Thymus	Thymus
47	chr6:12115800-12120400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:12116000-12128000	Weak transcription	Fetal Heart	heart
49	chr6:12116800-12120200	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr6:12116800-12120400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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