Variant report

Variant	rs6804970
Chromosome Location	chr3:49804290-49804291
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	chr3:49798677..49801501-chr3:49803723..49806643,2	K562	blood:
2	chr3:49797751..49801501-chr3:49803723..49807422,3	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11130217	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11709734	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11720705	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12715437	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13091525	1.00[ASN][1000 genomes]
rs1491985	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17304079	1.00[ASN][1000 genomes]
rs1799844	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996663	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1996664	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28535523	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3020779	0.83[EUR][1000 genomes]
rs35012435	1.00[ASN][1000 genomes]
rs35129566	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375092	1.00[ASN][1000 genomes]
rs35491931	1.00[ASN][1000 genomes]
rs35849525	1.00[ASN][1000 genomes]
rs55997059	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58339610	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59357103	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59684465	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61557789	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62260663	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260720	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260723	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62260755	1.00[ASN][1000 genomes]
rs62262061	1.00[ASN][1000 genomes]
rs62262106	1.00[ASN][1000 genomes]
rs62262118	1.00[ASN][1000 genomes]
rs62262722	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262730	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787892	1.00[ASN][1000 genomes]
rs6790568	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6809879	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71326904	1.00[ASN][1000 genomes]
rs7613603	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615318	1.00[ASN][1000 genomes]
rs7620848	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621797	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628207	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7635601	1.00[ASN][1000 genomes]
rs7637711	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649428	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829155	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835157	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836756	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851651	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870755	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870858	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6804970	AMT	cis	Thyroid	GTEx
rs6804970	RNF123	cis	Artery Tibial	GTEx
rs6804970	AMT	cis	lung	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49762600-49809000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:49775600-49817000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:49775800-49810200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr3:49775800-49823000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:49776400-49812000	Weak transcription	HSMM	muscle
6	chr3:49776400-49812200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:49776400-49812600	Weak transcription	Gastric	stomach
8	chr3:49776400-49818000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:49776400-49818000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:49776400-49818200	Weak transcription	Fetal Kidney	kidney
11	chr3:49776600-49812000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:49782600-49814000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:49785200-49807200	Weak transcription	Hela-S3	cervix
14	chr3:49785600-49822400	Weak transcription	HSMMtube	muscle
15	chr3:49785600-49822600	Weak transcription	Esophagus	oesophagus
16	chr3:49785800-49807400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:49785800-49811200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:49785800-49812400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:49785800-49818000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:49786000-49807200	Weak transcription	Fetal Brain Female	brain
21	chr3:49786000-49812400	Weak transcription	NHEK	skin
22	chr3:49786000-49812600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:49786000-49812800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:49786000-49814400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:49786000-49823000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:49786200-49806800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:49786200-49807400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:49786200-49812000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:49786200-49812600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:49786200-49812600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:49786200-49822400	Weak transcription	HMEC	breast
32	chr3:49786400-49817800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:49786600-49807400	Weak transcription	Aorta	Aorta
34	chr3:49786600-49812800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:49786600-49817800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:49787600-49807000	Weak transcription	Dnd41	blood
37	chr3:49787600-49808000	Weak transcription	Brain Germinal Matrix	brain
38	chr3:49787800-49807200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:49787800-49807200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:49787800-49812600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:49787800-49812600	Weak transcription	Thymus	Thymus
42	chr3:49788000-49807000	Weak transcription	Primary T cells from cord blood	blood
43	chr3:49788000-49807200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:49788400-49808600	Weak transcription	GM12878-XiMat	blood
45	chr3:49789600-49806200	Weak transcription	Placenta	Placenta
46	chr3:49789600-49806400	Weak transcription	Fetal Lung	lung
47	chr3:49791400-49812000	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:49791800-49812400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:49792000-49807000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:49792000-49807800	Weak transcription	Lung	lung

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