Variant report

Variant	rs6808044
Chromosome Location	chr3:50136165-50136166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50136072-50136644	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:50136118-50136552	GM12892	blood:	n/a	n/a
3	POLR2A	chr3:50136097-50136748	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:50132278-50136178	K562	blood:	n/a	n/a

Variant related genes	Relation type
RBM5	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs1061474	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1138536	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12107768	0.87[ASN][1000 genomes]
rs13095697	0.80[AFR][1000 genomes]
rs2240328	0.90[ASN][1000 genomes]
rs2247510	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2526747	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2526749	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2526750	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2624815	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2624817	0.90[ASN][1000 genomes]
rs2624822	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2624826	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2624829	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2624834	0.90[ASN][1000 genomes]
rs2624848	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2856237	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2856238	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34312088	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3774734	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4688753	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4688754	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6446194	0.82[ASN][1000 genomes]
rs6446195	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6446197	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6762477	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793528	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6799579	0.87[ASN][1000 genomes]
rs7061	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7430334	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7634441	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7648652	0.81[AFR][1000 genomes]
rs9682295	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
5	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS 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	24 gene(s)	inside rSNPs	diseases
6	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6808044	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs6808044	RBM6	cis	Whole Blood	GTEx
rs6808044	RBM6	cis	Heart Left Ventricle	GTEx
rs6808044	RBM6	cis	Esophagus Mucosa	GTEx
rs6808044	RBM6	cis	Esophagus Muscularis	GTEx
rs6808044	RBM6	cis	Artery Aorta	GTEx
rs6808044	RBM6	cis	lung	GTEx
rs6808044	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs6808044	RBM6	cis	Nerve Tibial	GTEx
rs6808044	RBM6	cis	Adipose Subcutaneous	GTEx
rs6808044	RBM6	cis	Artery Tibial	GTEx
rs6808044	RBM6	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50127400-50150000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:50127800-50157800	Strong transcription	H9 Cell Line	embryonic stem cell
3	chr3:50128000-50152600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:50128000-50157800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:50128000-50158000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:50128000-50158000	Strong transcription	Fetal Muscle Trunk	muscle
7	chr3:50128200-50152800	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr3:50128200-50158800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:50128400-50148800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:50128400-50157800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:50128400-50158200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:50128400-50158400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:50128400-50159000	Strong transcription	Lung	lung
14	chr3:50128600-50137400	Weak transcription	Right Atrium	heart
15	chr3:50128600-50137400	Strong transcription	HSMM	muscle
16	chr3:50128600-50137400	Strong transcription	HSMMtube	muscle
17	chr3:50128600-50138000	Strong transcription	Small Intestine	intestine
18	chr3:50128600-50141600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:50128600-50148800	Strong transcription	Fetal Muscle Leg	muscle
20	chr3:50128600-50156200	Strong transcription	Ovary	ovary
21	chr3:50128600-50158000	Strong transcription	NH-A	brain
22	chr3:50128600-50158400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:50128600-50158400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:50128600-50158600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:50128600-50158600	Strong transcription	Colonic Mucosa	Colon
26	chr3:50128600-50158800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:50128600-50158800	Strong transcription	Brain Germinal Matrix	brain
28	chr3:50128600-50158800	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr3:50128600-50159000	Strong transcription	Brain Angular Gyrus	brain
30	chr3:50128600-50159000	Strong transcription	Placenta	Placenta
31	chr3:50128600-50159000	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:50128600-50159200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:50128600-50159200	Strong transcription	Liver	Liver
34	chr3:50128600-50159200	Strong transcription	NHEK	skin
35	chr3:50128600-50160400	Strong transcription	Fetal Thymus	thymus
36	chr3:50128800-50137400	Strong transcription	Fetal Lung	lung
37	chr3:50128800-50149000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:50128800-50156600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:50128800-50156600	Strong transcription	Brain Substantia Nigra	brain
40	chr3:50128800-50158600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:50128800-50158600	Strong transcription	HMEC	breast
42	chr3:50128800-50159000	Strong transcription	Brain Anterior Caudate	brain
43	chr3:50129000-50137400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:50129000-50137600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:50129000-50141600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:50129000-50158600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:50129000-50158600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr3:50129000-50158800	Strong transcription	Fetal Intestine Large	intestine
49	chr3:50129000-50159000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:50129000-50159200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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