Variant report

Variant	rs1975844
Chromosome Location	chr3:48442959-48442960
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48442729..48446947-chr3:48464942..48468489,4	MCF-7	breast:
2	chr3:48389115..48391524-chr3:48440665..48443263,2	MCF-7	breast:
3	chr3:48442075..48446343-chr3:48473380..48477493,6	MCF-7	breast:
4	chr3:48442321..48445623-chr3:48469193..48472197,3	MCF-7	breast:
5	chr3:48441736..48444624-chr3:48460288..48462791,2	MCF-7	breast:
6	chr3:48441632..48443012-chr3:48477036..48477951,7	MCF-7	breast:
7	chr3:48313829..48315747-chr3:48442766..48445683,2	MCF-7	breast:
8	chr3:48441909..48442996-chr3:48477024..48478037,12	K562	blood:
9	chr3:48440673..48446097-chr3:48469254..48474939,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000164050	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1037773	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10470686	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109227	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11130170	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130171	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11712561	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11797	0.86[EUR][1000 genomes]
rs12487542	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13069724	0.96[EUR][1000 genomes]
rs13071337	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13072012	0.90[EUR][1000 genomes]
rs13076076	0.97[EUR][1000 genomes]
rs13091785	0.94[EUR][1000 genomes]
rs13314659	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324374	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1459242	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1459249	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1459250	0.90[EUR][1000 genomes]
rs1563736	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1870444	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2045554	0.93[EUR][1000 genomes]
rs2242150	0.93[EUR][1000 genomes]
rs2279077	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2290822	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2362450	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2362452	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28824259	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2885509	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2885510	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3214041	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34761139	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35215722	0.91[EUR][1000 genomes]
rs3774808	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4490383	0.92[EUR][1000 genomes]
rs4858793	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4858817	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56298324	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60512868	0.96[EUR][1000 genomes]
rs6442116	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442117	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442118	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442119	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442120	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6442123	0.93[EUR][1000 genomes]
rs6442124	0.84[EUR][1000 genomes]
rs6764415	0.82[EUR][1000 genomes]
rs6770470	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6776700	0.93[EUR][1000 genomes]
rs6779262	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6784322	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6784541	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6794875	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6796491	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6800475	0.94[EUR][1000 genomes]
rs6804774	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6810060	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7126	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs725309	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs725310	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73074358	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618883	0.90[EUR][1000 genomes]
rs7630741	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7634377	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7635522	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7636044	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7636782	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7639743	0.90[EUR][1000 genomes]
rs7653691	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs898225	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs922075	0.92[EUR][1000 genomes]
rs9311423	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311424	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9809843	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9812647	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815103	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9817615	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9826195	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9826247	0.93[EUR][1000 genomes]
rs9838618	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9849509	0.96[EUR][1000 genomes]
rs9862575	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9864371	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9864815	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9875280	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9876781	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9876891	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9881491	0.94[EUR][1000 genomes]
rs9883759	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9883927	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1975844	TMA7	cis	Muscle Skeletal	GTEx
rs1975844	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs1975844	RP11-24C3.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48435400-48449800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:48439200-48443000	Weak transcription	HUVEC	blood vessel
3	chr3:48439400-48445000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:48439400-48447800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:48440000-48443000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:48440000-48443800	Weak transcription	Lung	lung
7	chr3:48440000-48444000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:48440200-48443000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:48440200-48444800	Weak transcription	Fetal Lung	lung
10	chr3:48440400-48443800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:48440400-48443800	Weak transcription	Spleen	Spleen
12	chr3:48440400-48444200	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:48440400-48444200	Weak transcription	Brain Substantia Nigra	brain
14	chr3:48440600-48443000	Weak transcription	Aorta	Aorta
15	chr3:48440600-48444400	Enhancers	Esophagus	oesophagus
16	chr3:48440800-48443000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:48440800-48443000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:48440800-48443600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:48440800-48444000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:48440800-48444000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:48440800-48447800	Weak transcription	Fetal Kidney	kidney
22	chr3:48441000-48443000	Weak transcription	Fetal Stomach	stomach
23	chr3:48441000-48444200	Weak transcription	Brain Anterior Caudate	brain
24	chr3:48441000-48444400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:48441200-48443000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:48441200-48443000	Weak transcription	HSMMtube	muscle
27	chr3:48441200-48443200	Weak transcription	Hela-S3	cervix
28	chr3:48441200-48444200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:48441200-48444600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:48441400-48443600	Weak transcription	HepG2	liver
31	chr3:48441400-48444400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:48441600-48443000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:48441600-48443000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:48441600-48443200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr3:48441600-48443400	Weak transcription	Liver	Liver
36	chr3:48441600-48443800	Weak transcription	Fetal Intestine Large	intestine
37	chr3:48441600-48443800	Weak transcription	Pancreas	Pancrea
38	chr3:48441600-48444800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:48441600-48445200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:48441800-48443000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:48441800-48443800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:48441800-48445000	Weak transcription	Fetal Muscle Leg	muscle
43	chr3:48442000-48443800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:48442000-48443800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:48442000-48443800	Weak transcription	Fetal Brain Female	brain
46	chr3:48442000-48444800	Genic enhancers	HMEC	breast
47	chr3:48442000-48466200	Strong transcription	Fetal Intestine Small	intestine
48	chr3:48442000-48467400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:48442200-48443000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:48442200-48464600	Strong transcription	Brain Germinal Matrix	brain

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