Variant report

Variant	rs2471343
Chromosome Location	chr4:3042902-3042903
allele	G/T
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	TBP	chr4:3042839-3044161	GM12878	blood:	n/a	n/a
2	YY1	chr4:3042831-3043485	GM12891	blood:	n/a	n/a
3	TCF12	chr4:3042818-3043324	GM12878	blood:	n/a	n/a
4	MTA3	chr4:3042029-3044138	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:3042210-3043957	GM18526	blood:	n/a	n/a
6	POLR2A	chr4:3042151-3043922	GM12892	blood:	n/a	n/a
7	POLR2A	chr4:3042178-3044027	GM12892	blood:	n/a	n/a
8	CUX1	chr4:3042879-3043351	GM12878	blood:	n/a	n/a
9	EBF1	chr4:3042143-3043940	GM12878	blood:	n/a	chr4:3043105-3043116
10	RUNX3	chr4:3041924-3043896	GM12878	blood:	n/a	n/a
11	RUNX3	chr4:3041863-3044165	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:3042215-3043929	GM18951	blood:	n/a	n/a
13	POLR2A	chr4:3042817-3043955	GM12891	blood:	n/a	n/a
14	BCLAF1	chr4:3042817-3043402	GM12878	blood:	n/a	chr4:3042925-3042934 chr4:3043222-3043235
15	POLR2A	chr4:3041640-3044734	GM12891	blood:	n/a	n/a
16	FOXM1	chr4:3042146-3043263	GM12878	blood:	n/a	n/a
17	POLR2A	chr4:3042157-3044616	GM12878	blood:	n/a	n/a
18	PAX5	chr4:3042120-3043907	GM12878	blood:	n/a	chr4:3042244-3042253
19	POLR2A	chr4:3042135-3044075	GM12878	blood:	n/a	n/a
20	STAT5A	chr4:3042193-3043181	GM12878	blood:	n/a	chr4:3042796-3042808 chr4:3042244-3042255
21	POLR2A	chr4:3042204-3043918	GM10847	blood:	n/a	n/a
22	POLR2A	chr4:3042124-3044657	GM18505	blood:	n/a	n/a
23	POLR2A	chr4:3042827-3043934	GM12891	blood:	n/a	n/a
24	BHLHE40	chr4:3042034-3044019	GM12878	blood:	n/a	chr4:3043518-3043534 chr4:3043900-3043916 chr4:3043010-3043026
25	CHD1	chr4:3042158-3043826	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:3042193-3044036	GM12892	blood:	n/a	n/a
27	ELF1	chr4:3042019-3044065	GM12878	blood:	n/a	chr4:3042273-3042285
28	STAT5A	chr4:3042848-3043446	GM12878	blood:	n/a	chr4:3043388-3043400
29	MTA3	chr4:3042156-3043414	GM12878	blood:	n/a	n/a
30	POLR2A	chr4:3042852-3043897	GM12878	blood:	n/a	n/a
31	POLR2A	chr4:3042174-3043956	GM12891	blood:	n/a	n/a
32	POLR2A	chr4:3042829-3043945	GM12892	blood:	n/a	n/a
33	UBTF	chr4:3042885-3043252	K562	blood:	n/a	n/a
34	CHD2	chr4:3042277-3043745	GM12878	blood:	n/a	n/a
35	MAX	chr4:3042171-3043968	GM12878	blood:	n/a	chr4:3043238-3043246
36	TCF3	chr4:3042354-3043905	GM12878	blood:	n/a	chr4:3043751-3043765 chr4:3043892-3043902
37	POLR2A	chr4:3042171-3044373	GM19193	blood:	n/a	n/a
38	ELK1	chr4:3042757-3042942	GM12878	blood:	n/a	n/a
39	CTCF	chr4:3042900-3043050	GM12864	blood:	n/a	chr4:3043009-3043017
40	YY1	chr4:3042786-3044020	GM12878	blood:	n/a	chr4:3043534-3043548 chr4:3043511-3043525 chr4:3043525-3043539
41	POLR2A	chr4:3042121-3044005	GM15510	blood:	n/a	n/a
42	SIN3A	chr4:3042692-3043182	GM12878	blood:	n/a	n/a
43	POLR2A	chr4:3042519-3043957	GM12878	blood:	n/a	n/a
44	CTCF	chr4:3042780-3042930	GM12873	blood:	n/a	n/a
45	RELA	chr4:3042188-3044252	GM15510	blood:	n/a	n/a
46	MAX	chr4:3042888-3043121	K562	blood:	n/a	n/a
47	NFIC	chr4:3041854-3043903	GM12878	blood:	n/a	n/a
48	MXI1	chr4:3042832-3043978	GM12878	blood:	n/a	n/a
49	POLR2A	chr4:3042166-3044058	GM19099	blood:	n/a	n/a
50	ZEB1	chr4:3042789-3043179	GM12878	blood:	n/a	chr4:3043012-3043021

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3038898..3040591-chr4:3042630..3044225,2	K562	blood:

Variant related genes	Relation type
RNU6-204P	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10000252	1.00[CEU][hapmap]
rs10002065	1.00[CEU][hapmap]
rs10009229	1.00[CEU][hapmap]
rs10009935	1.00[CEU][hapmap]
rs10010375	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10011127	1.00[CEU][hapmap]
rs10011412	1.00[CEU][hapmap]
rs10014333	1.00[CEU][hapmap]
rs10016755	1.00[CEU][hapmap]
rs1419036	1.00[CEU][hapmap]
rs16843866	1.00[CEU][hapmap]
rs16843869	1.00[CEU][hapmap]
rs2471348	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2488811	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2515931	1.00[CEU][hapmap]
rs2515934	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2515955	0.96[EUR][1000 genomes]
rs2515956	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28795684	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28856696	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2960299	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2995802	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs3021124	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs363138	1.00[CEU][hapmap]
rs61269488	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7693317	1.00[CEU][hapmap]
rs9291159	1.00[CEU][hapmap]
rs9991144	1.00[CEU][hapmap]

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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv1013440	chr4:2993130-3053503	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2471343	RCN3	trans	lymphoblastoid	seeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3021200-3043000	Weak transcription	Brain Germinal Matrix	brain
2	chr4:3025200-3043400	Weak transcription	Aorta	Aorta
3	chr4:3039400-3043000	Weak transcription	Pancreas	Pancrea
4	chr4:3039800-3043000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:3039800-3043000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr4:3039800-3043200	Weak transcription	Fetal Kidney	kidney
7	chr4:3040000-3043000	Weak transcription	Psoas Muscle	Psoas
8	chr4:3040000-3043000	Weak transcription	Right Atrium	heart
9	chr4:3040200-3043000	Weak transcription	Brain Substantia Nigra	brain
10	chr4:3040200-3043000	Weak transcription	Right Ventricle	heart
11	chr4:3040200-3043200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr4:3040600-3043000	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:3040600-3043000	Weak transcription	Fetal Lung	lung
14	chr4:3040600-3043000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:3040600-3043000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:3040600-3043400	Weak transcription	Small Intestine	intestine
17	chr4:3040600-3043600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:3040800-3043000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr4:3041800-3043000	Enhancers	Fetal Muscle Leg	muscle
20	chr4:3041800-3044400	Flanking Active TSS	Primary B cells from peripheral blood	blood
21	chr4:3042200-3043000	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr4:3042200-3043400	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr4:3042200-3043400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr4:3042200-3044400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr4:3042400-3043000	Enhancers	Primary hematopoietic stem cells	blood
26	chr4:3042400-3043000	Enhancers	Placenta	Placenta
27	chr4:3042400-3043000	Enhancers	Spleen	Spleen
28	chr4:3042400-3043000	Enhancers	NHDF-Ad	bronchial
29	chr4:3042400-3043400	Flanking Active TSS	Colonic Mucosa	Colon
30	chr4:3042400-3044600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:3042400-3044600	Flanking Active TSS	GM12878-XiMat	blood
32	chr4:3042600-3043000	Enhancers	Primary T cells from cord blood	blood
33	chr4:3042600-3043000	Enhancers	Ovary	ovary
34	chr4:3042600-3043000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
35	chr4:3042600-3043200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
36	chr4:3042600-3043200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr4:3042600-3043200	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr4:3042600-3043800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:3042600-3044000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:3042600-3044000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr4:3042600-3044200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
42	chr4:3042600-3044600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr4:3042600-3044600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr4:3042800-3043000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:3042800-3043000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:3042800-3043000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:3042800-3043000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr4:3042800-3043000	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr4:3042800-3043000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:3042800-3043000	Enhancers	Liver	Liver

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