Variant report

Variant	rs2352984
Chromosome Location	chr3:49948728-49948729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49938059..49942397-chr3:49945875..49951610,6	K562	blood:
2	chr3:49939809..49942397-chr3:49948485..49950283,3	K562	blood:
3	chr3:49942811..49946038-chr3:49946373..49949588,4	K562	blood:

Variant related genes	Relation type
ENSG00000228008	Chromatin interaction
ENSG00000164078	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10049087	0.81[JPT][hapmap]
rs1061474	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1062633	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs10865959	0.86[CHB][hapmap]
rs11130222	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130224	0.81[AMR][1000 genomes]
rs11130228	0.81[JPT][hapmap]
rs11130233	0.89[JPT][hapmap]
rs11706185	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11709503	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11709573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11712056	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11713193	0.81[AMR][1000 genomes]
rs11714324	0.93[ASN][1000 genomes]
rs11721204	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12496973	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs12634780	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13060128	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs13077403	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13079006	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13082703	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1317140	0.89[CHB][hapmap]
rs17657664	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17657688	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1799843	0.89[CHB][hapmap]
rs1799845	0.89[CHB][hapmap]
rs2013208	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2230590	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2240326	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2240327	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2240328	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2240329	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2247510	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap]
rs2252833	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2276864	0.86[CHB][hapmap]
rs2280406	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2352969	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2352975	0.89[CHB][hapmap]
rs2353579	0.82[JPT][hapmap]
rs2526747	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs2526748	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2526749	0.82[AFR][1000 genomes]
rs2526750	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2526751	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2526754	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2624819	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2624821	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2624822	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2624832	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2624834	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2624843	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2624853	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2681776	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2681779	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs2681780	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2681781	0.89[CHD][hapmap];0.82[JPT][hapmap]
rs2777888	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2856234	0.90[CHD][hapmap]
rs2883057	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs2883059	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34034116	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34312088	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34654589	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35275715	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36022378	0.86[ASN][1000 genomes]
rs3733134	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3774733	0.82[JPT][hapmap]
rs3774734	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3774759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796386	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4688688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4688689	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs4688690	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs4688753	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4688755	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs4688758	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs55692411	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62262114	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6446191	0.81[AFR][1000 genomes]
rs6446193	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs6446194	0.83[AFR][1000 genomes]
rs6762477	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs6765484	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs6771546	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs6772095	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs6774354	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792892	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs6793528	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6795703	0.81[AMR][1000 genomes]
rs7061	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7430334	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7613360	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7613875	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs7615206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7621026	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs7621352	0.82[JPT][hapmap]
rs7626952	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7627864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7627910	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7628058	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs7629936	0.89[CHB][hapmap]
rs7634441	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7648174	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs868891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311446	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs952594	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9814664	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs9821675	0.90[JPT][hapmap]
rs9861216	0.90[CHD][hapmap];0.82[JPT][hapmap]
rs9866695	0.90[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh 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	90 gene(s)	inside rSNPs	diseases
2	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
3	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS 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	47 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs2352984	RBM6	cis	lymphoblastoid	seeQTL
rs2352984	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs2352984	RBM6	cis	Artery Aorta	GTEx
rs2352984	RBM6	cis	lung	GTEx
rs2352984	RBM6	cis	Esophagus Mucosa	GTEx
rs2352984	ARIH2	cis	cerebellum	SCAN
rs2352984	RBM6	cis	Esophagus Muscularis	GTEx
rs2352984	RBM6	cis	Thyroid	GTEx
rs2352984	QRICH1	cis	cerebellum	SCAN
rs2352984	RBM6	cis	cerebellum	SCAN
rs2352984	RBM6	cis	Whole Blood	GTEx
rs2352984	RNF123	cis	parietal	SCAN
rs2352984	RBM6	cis	Artery Tibial	GTEx
rs2352984	RBM6	cis	Adipose Subcutaneous	GTEx
rs2352984	RBM6	cis	parietal	SCAN
rs2352984	RBM6	cis	Nerve Tibial	GTEx
rs2352984	RBM6	cis	Heart Left Ventricle	GTEx
rs2352984	CELSR3	cis	parietal	SCAN
rs2352984	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs2352984	RNF123	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49941800-49950200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:49943600-49950800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:49943800-49966000	Weak transcription	Psoas Muscle	Psoas
4	chr3:49944000-49949400	Weak transcription	Right Atrium	heart
5	chr3:49944000-49954000	Weak transcription	NHDF-Ad	bronchial
6	chr3:49944200-49948800	Weak transcription	HSMMtube	muscle
7	chr3:49944200-49949800	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:49944200-49956200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:49944200-49962000	Weak transcription	HepG2	liver
10	chr3:49944200-49962000	Weak transcription	HSMM	muscle
11	chr3:49944200-49962000	Weak transcription	NH-A	brain
12	chr3:49944200-49966000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:49944400-49948800	Weak transcription	Primary B cells from cord blood	blood
14	chr3:49944400-49950400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:49944400-49950600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:49944400-49952600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:49944400-49952800	Weak transcription	GM12878-XiMat	blood
18	chr3:49944400-49955000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:49944400-49966000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:49944400-49966000	Weak transcription	HUVEC	blood vessel
21	chr3:49944600-49949600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:49944600-49950800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:49944600-49961800	Weak transcription	Hela-S3	cervix
24	chr3:49944800-49951400	Strong transcription	Fetal Muscle Leg	muscle
25	chr3:49945000-49950800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:49945200-49950800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr3:49945200-49950800	Strong transcription	Fetal Stomach	stomach
28	chr3:49945400-49950800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:49945400-49950800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:49945400-49950800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:49945400-49950800	Strong transcription	Thymus	Thymus
32	chr3:49945400-49951000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:49945600-49950000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:49945600-49950600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:49945600-49950800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:49945600-49950800	Strong transcription	Fetal Brain Female	brain
37	chr3:49945600-49950800	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:49945600-49950800	Strong transcription	Dnd41	blood
39	chr3:49945600-49951000	Strong transcription	Primary T cells from cord blood	blood
40	chr3:49945600-49951400	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr3:49945800-49949400	Strong transcription	Brain Hippocampus Middle	brain
42	chr3:49945800-49950600	Strong transcription	Small Intestine	intestine
43	chr3:49945800-49950800	Strong transcription	Brain Cingulate Gyrus	brain
44	chr3:49945800-49950800	Strong transcription	Stomach Smooth Muscle	stomach
45	chr3:49945800-49950800	Strong transcription	Spleen	Spleen
46	chr3:49946000-49949600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:49946000-49949800	Strong transcription	Esophagus	oesophagus
48	chr3:49946000-49950000	Strong transcription	Adipose Nuclei	Adipose
49	chr3:49946000-49950400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:49946000-49950600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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