Variant report

Variant	rs11721204
Chromosome Location	chr3:49982765-49982766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49976777..49979438-chr3:49981879..49983606,2	MCF-7	breast:
2	chr3:49977713..49979508-chr3:49980727..49984411,5	K562	blood:
3	chr3:49977713..49979804-chr3:49979930..49983021,3	K562	blood:

Variant related genes	Relation type
ENSG00000004534	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11130222	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11706185	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11709503	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11709573	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712056	0.89[ASN][1000 genomes]
rs11714324	0.95[ASN][1000 genomes]
rs12634780	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13077403	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13079006	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13082703	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17657664	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17657688	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2352969	0.95[ASN][1000 genomes]
rs2352984	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2526747	0.80[ASN][1000 genomes]
rs2526750	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2624815	0.80[ASN][1000 genomes]
rs2624819	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2624821	0.91[ASN][1000 genomes]
rs2624832	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2681776	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2681779	0.81[ASN][1000 genomes]
rs2883059	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34034116	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34312088	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34654589	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35275715	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36022378	0.87[ASN][1000 genomes]
rs3733134	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774759	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796386	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4688688	0.88[ASN][1000 genomes]
rs4688753	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4688754	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55692411	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62262114	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6446191	0.83[EUR][1000 genomes]
rs6446192	0.81[EUR][1000 genomes]
rs6446194	0.80[EUR][1000 genomes]
rs6446195	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6762477	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6774354	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793528	0.80[ASN][1000 genomes]
rs7430334	0.80[ASN][1000 genomes]
rs7613360	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7615206	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626952	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7627864	0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7627910	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7634441	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7648174	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs868891	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs952594	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9682295	0.80[EUR][1000 genomes];0.80[ASN][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	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv965334	chr3:49967342-50000012	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11721204	RBM6	cis	Thyroid	GTEx
rs11721204	RBM6	cis	Nerve Tibial	GTEx
rs11721204	RBM6	cis	Whole Blood	GTEx
rs11721204	RBM6	cis	Esophagus Mucosa	GTEx
rs11721204	RBM6	cis	Esophagus Muscularis	GTEx
rs11721204	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs11721204	RBM6	cis	Adipose Subcutaneous	GTEx
rs11721204	RBM6	cis	Artery Tibial	GTEx
rs11721204	RBM6	cis	lung	GTEx
rs11721204	RBM6	cis	Artery Aorta	GTEx
rs11721204	RBM6	cis	Heart Left Ventricle	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49978600-49983000	Weak transcription	Lung	lung
2	chr3:49978600-49986400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:49978600-49986800	Weak transcription	Left Ventricle	heart
4	chr3:49978600-49988800	Weak transcription	Aorta	Aorta
5	chr3:49978800-49982800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:49978800-49983200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:49978800-49983400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:49978800-49985400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:49978800-49986800	Weak transcription	Stomach Mucosa	stomach
10	chr3:49978800-49987000	Weak transcription	Small Intestine	intestine
11	chr3:49978800-49987400	Weak transcription	Brain Anterior Caudate	brain
12	chr3:49978800-49987400	Weak transcription	K562	blood
13	chr3:49978800-49987600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:49978800-49987600	Weak transcription	Brain Substantia Nigra	brain
15	chr3:49978800-49987600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:49978800-49987600	Weak transcription	A549	lung
17	chr3:49978800-49987600	Weak transcription	HUVEC	blood vessel
18	chr3:49978800-49987800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:49978800-50000600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:49978800-50004800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:49978800-50009600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:49978800-50009600	Weak transcription	Fetal Kidney	kidney
23	chr3:49978800-50041000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:49979000-49982800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:49979000-49982800	Weak transcription	Fetal Intestine Large	intestine
26	chr3:49979000-49982800	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:49979000-49983200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:49979000-49984800	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:49979000-49985800	Weak transcription	Esophagus	oesophagus
30	chr3:49979000-49986800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:49979000-49987000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:49979000-49987400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:49979000-49987400	Weak transcription	Gastric	stomach
34	chr3:49979000-49987400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:49979000-49987400	Weak transcription	Hela-S3	cervix
36	chr3:49979000-49987400	Weak transcription	NH-A	brain
37	chr3:49979000-49987400	Weak transcription	NHEK	skin
38	chr3:49979000-49987600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:49979000-49987600	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:49979000-49987600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr3:49979000-49987600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr3:49979000-49987600	Weak transcription	Fetal Heart	heart
43	chr3:49979000-49987600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:49979000-49987600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:49979000-49987600	Weak transcription	HMEC	breast
46	chr3:49979000-49987800	Weak transcription	Pancreas	Pancrea
47	chr3:49979000-49988800	Weak transcription	Spleen	Spleen
48	chr3:49979000-49990200	Weak transcription	Fetal Lung	lung
49	chr3:49979000-49990600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:49979000-49994600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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