Variant report

Variant	rs6446191
Chromosome Location	chr3:50052834-50052835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11706185	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11709503	0.88[EUR][1000 genomes]
rs11721204	0.83[EUR][1000 genomes]
rs12634780	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13077403	0.89[EUR][1000 genomes]
rs13079006	0.87[EUR][1000 genomes]
rs13082703	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17657664	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17657688	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2352984	0.81[AFR][1000 genomes]
rs2526749	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2526750	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2624815	0.81[EUR][1000 genomes]
rs2624819	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2624822	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2624832	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2681776	0.92[EUR][1000 genomes]
rs34312088	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3774734	0.81[EUR][1000 genomes]
rs4688753	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4688754	0.86[EUR][1000 genomes]
rs6446190	0.82[ASN][1000 genomes]
rs6446192	0.88[EUR][1000 genomes]
rs6446194	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6446195	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6446197	0.84[AFR][1000 genomes]
rs6762477	0.81[EUR][1000 genomes]
rs6793528	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7430334	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7626952	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7627910	0.81[EUR][1000 genomes]
rs7634441	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7645466	0.92[AMR][1000 genomes]
rs7648174	0.90[EUR][1000 genomes]
rs9682295	0.83[EUR][1000 genomes]
rs9812936	0.83[EUR][1000 genomes]
rs9844201	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv460527	chr3:50028385-50153356	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv590249	chr3:50028385-50153356	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6446191	RBM6	cis	Esophagus Mucosa	GTEx
rs6446191	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs6446191	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs6446191	RBM6	cis	Nerve Tibial	GTEx
rs6446191	RBM6	cis	lung	GTEx
rs6446191	RBM6	cis	Thyroid	GTEx
rs6446191	RBM6	cis	Heart Left Ventricle	GTEx
rs6446191	RBM6	cis	Artery Tibial	GTEx
rs6446191	RBM6	cis	Artery Aorta	GTEx
rs6446191	RBM6	cis	Esophagus Muscularis	GTEx
rs6446191	RBM6	cis	Adipose Subcutaneous	GTEx
rs6446191	RBM6	cis	Whole Blood	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:49998400-50078600	Weak transcription	K562	blood
3	chr3:50002200-50057000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
5	chr3:50010800-50087000	Weak transcription	NHLF	lung
6	chr3:50011000-50078400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon
8	chr3:50015200-50092000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:50028000-50056400	Weak transcription	Ovary	ovary
10	chr3:50028800-50082600	Weak transcription	Right Ventricle	heart
11	chr3:50030200-50065600	Weak transcription	Fetal Heart	heart
12	chr3:50035200-50058200	Weak transcription	Esophagus	oesophagus
13	chr3:50036600-50085600	Weak transcription	HUVEC	blood vessel
14	chr3:50036800-50054600	Strong transcription	Fetal Intestine Small	intestine
15	chr3:50037200-50087000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:50037600-50055400	Weak transcription	Hela-S3	cervix
17	chr3:50037600-50061800	Weak transcription	Small Intestine	intestine
18	chr3:50038400-50084600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:50038600-50087400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:50038800-50056800	Weak transcription	HepG2	liver
21	chr3:50039400-50061800	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:50039400-50084600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:50040400-50056000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:50041400-50053400	Weak transcription	Fetal Lung	lung
25	chr3:50041400-50057000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:50041400-50095200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:50041600-50053400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:50041600-50055200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:50041600-50056800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:50041600-50057000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:50041600-50058200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:50041600-50061600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:50041600-50063000	Weak transcription	Brain Substantia Nigra	brain
34	chr3:50041600-50065200	Weak transcription	NH-A	brain
35	chr3:50041600-50085000	Weak transcription	Fetal Brain Female	brain
36	chr3:50041600-50085400	Weak transcription	Brain Angular Gyrus	brain
37	chr3:50041600-50093400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:50041800-50085200	Weak transcription	Fetal Brain Male	brain
39	chr3:50042400-50054600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:50043400-50085200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:50044000-50057400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:50044400-50053400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:50045200-50085000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:50046200-50059000	Strong transcription	Dnd41	blood
45	chr3:50046600-50055600	Weak transcription	HSMMtube	muscle
46	chr3:50046800-50053400	Weak transcription	GM12878-XiMat	blood
47	chr3:50046800-50053600	Weak transcription	Adipose Nuclei	Adipose
48	chr3:50046800-50056200	Weak transcription	NHEK	skin
49	chr3:50046800-50056600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:50046800-50056600	Weak transcription	Osteobl	bone

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