Variant report

Variant	rs2301166
Chromosome Location	chr3:50148305-50148306
allele	C/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	chr3:50147543-50148327	GM12878	blood:	n/a	n/a
2	E2F4	chr3:50148125-50148359	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49899384..49901506-chr3:50147689..50150023,2	K562	blood:

Variant related genes	Relation type
RBM5	TF binding region
ENSG00000164076	Chromatin interaction
ENSG00000264706	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10049087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1061474	0.81[JPT][hapmap]
rs11130228	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs11130233	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1138536	0.81[JPT][hapmap]
rs11713562	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12496973	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs13060128	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs2008877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2013208	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071206	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071207	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2236939	0.90[JPT][hapmap]
rs2240326	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240329	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2245365	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2252833	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap]
rs2353579	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs2526743	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2526748	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2526751	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2526754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2624816	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2624823	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2624824	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2624825	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2624826	0.81[JPT][hapmap]
rs2624843	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap]
rs2624847	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2624853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2856234	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2856236	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[EUR][1000 genomes]
rs2856237	0.81[JPT][hapmap]
rs2856238	0.81[JPT][hapmap]
rs2883057	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs34831713	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733133	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774733	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4688686	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688689	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4688690	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4688755	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4688758	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6446193	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.88[ASN][1000 genomes]
rs6446202	0.90[JPT][hapmap]
rs6765484	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes]
rs6771546	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs6772095	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6792892	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs739431	0.90[JPT][hapmap]
rs7428430	0.86[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7613875	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7621026	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs7621352	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7628058	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7642692	0.90[JPT][hapmap]
rs7642934	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9311446	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9810125	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9814664	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9856572	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9861216	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9866695	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
8	nsv818139	chr3:50144951-50174572	Weak transcription Strong transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2301166	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2301166	RBM6	cis	Stomach	GTEx
rs2301166	RBM6	cis	Whole Blood	GTEx
rs2301166	RBM6	cis	Artery Tibial	GTEx
rs2301166	RBM6	cis	Artery Aorta	GTEx
rs2301166	RBM6	cis	Esophagus Mucosa	GTEx
rs2301166	RBM6	cis	Heart Left Ventricle	GTEx
rs2301166	RBM6	cis	Adipose Subcutaneous	GTEx
rs2301166	RBM6	cis	Esophagus Muscularis	GTEx
rs2301166	RBM6	cis	Thyroid	GTEx
rs2301166	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs2301166	RBM6	cis	lung	GTEx
rs2301166	RBM6	cis	Nerve Tibial	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	chr3:50128600-50148800	Strong transcription	Fetal Muscle Leg	muscle
15	chr3:50128600-50156200	Strong transcription	Ovary	ovary
16	chr3:50128600-50158000	Strong transcription	NH-A	brain
17	chr3:50128600-50158400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:50128600-50158400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:50128600-50158600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:50128600-50158600	Strong transcription	Colonic Mucosa	Colon
21	chr3:50128600-50158800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:50128600-50158800	Strong transcription	Brain Germinal Matrix	brain
23	chr3:50128600-50158800	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr3:50128600-50159000	Strong transcription	Brain Angular Gyrus	brain
25	chr3:50128600-50159000	Strong transcription	Placenta	Placenta
26	chr3:50128600-50159000	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:50128600-50159200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:50128600-50159200	Strong transcription	Liver	Liver
29	chr3:50128600-50159200	Strong transcription	NHEK	skin
30	chr3:50128600-50160400	Strong transcription	Fetal Thymus	thymus
31	chr3:50128800-50149000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:50128800-50156600	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:50128800-50156600	Strong transcription	Brain Substantia Nigra	brain
34	chr3:50128800-50158600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:50128800-50158600	Strong transcription	HMEC	breast
36	chr3:50128800-50159000	Strong transcription	Brain Anterior Caudate	brain
37	chr3:50129000-50158600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:50129000-50158600	Strong transcription	Duodenum Mucosa	Duodenum
39	chr3:50129000-50158800	Strong transcription	Fetal Intestine Large	intestine
40	chr3:50129000-50159000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:50129000-50159200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:50129000-50159200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:50129000-50159400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:50129000-50159400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:50129000-50160000	Strong transcription	Fetal Stomach	stomach
46	chr3:50129000-50160000	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr3:50129000-50160800	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr3:50129200-50148400	Strong transcription	Hela-S3	cervix
49	chr3:50129200-50157600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:50129200-50158600	Strong transcription	Rectal Mucosa Donor 29	rectum

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