Variant report

Variant	rs2857849
Chromosome Location	chr4:3043638-3043639
allele	A/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	MTA3	chr4:3042029-3044138	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:3042210-3043957	GM18526	blood:	n/a	n/a
4	TAF1	chr4:3042966-3043921	GM12878	blood:	n/a	n/a
5	MAZ	chr4:3042927-3043926	GM12878	blood:	n/a	chr4:3043238-3043246
6	POLR2A	chr4:3042151-3043922	GM12892	blood:	n/a	n/a
7	POLR2A	chr4:3042989-3043872	GM12892	blood:	n/a	n/a
8	POLR2A	chr4:3042178-3044027	GM12892	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	YY1	chr4:3043206-3043961	HepG2	liver:	n/a	chr4:3043534-3043548 chr4:3043511-3043525 chr4:3043525-3043539
12	WRNIP1	chr4:3043549-3044268	GM12878	blood:	n/a	n/a
13	CHD2	chr4:3043512-3043884	HepG2	liver:	n/a	n/a
14	ZNF143	chr4:3042943-3043669	GM12878	blood:	n/a	chr4:3043525-3043535
15	RUNX3	chr4:3041863-3044165	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:3042215-3043929	GM18951	blood:	n/a	n/a
17	POLR2A	chr4:3042817-3043955	GM12891	blood:	n/a	n/a
18	POLR2A	chr4:3041640-3044734	GM12891	blood:	n/a	n/a
19	MAX	chr4:3043155-3043847	HepG2	liver:	n/a	chr4:3043238-3043246
20	BHLHE40	chr4:3043609-3043894	HepG2	liver:	n/a	n/a
21	POLR2A	chr4:3042157-3044616	GM12878	blood:	n/a	n/a
22	PAX5	chr4:3042120-3043907	GM12878	blood:	n/a	chr4:3042244-3042253
23	POLR2A	chr4:3042135-3044075	GM12878	blood:	n/a	n/a
24	POLR2A	chr4:3042204-3043918	GM10847	blood:	n/a	n/a
25	POLR2A	chr4:3042124-3044657	GM18505	blood:	n/a	n/a
26	POLR2A	chr4:3042827-3043934	GM12891	blood:	n/a	n/a
27	POLR2A	chr4:3043085-3043941	HUVEC	blood vessel:	n/a	n/a
28	BHLHE40	chr4:3042034-3044019	GM12878	blood:	n/a	chr4:3043518-3043534 chr4:3043900-3043916 chr4:3043010-3043026
29	EBF1	chr4:3042948-3043710	GM12878	blood:	n/a	chr4:3043105-3043116
30	CHD1	chr4:3042158-3043826	GM12878	blood:	n/a	n/a
31	SP1	chr4:3043597-3043955	GM12878	blood:	n/a	n/a
32	POLR2A	chr4:3042193-3044036	GM12892	blood:	n/a	n/a
33	ELF1	chr4:3042019-3044065	GM12878	blood:	n/a	chr4:3042273-3042285
34	STAT5A	chr4:3043307-3044252	GM12878	blood:	n/a	chr4:3043388-3043400 chr4:3044052-3044059
35	CTCF	chr4:3043520-3043670	HVMF	connective:	n/a	n/a
36	FOSL2	chr4:3043516-3043914	HepG2	liver:	n/a	n/a
37	PBX3	chr4:3043497-3043812	GM12878	blood:	n/a	n/a
38	POU2F2	chr4:3042918-3043998	GM12891	blood:	n/a	chr4:3043363-3043375 chr4:3043591-3043603
39	POLR2A	chr4:3042852-3043897	GM12878	blood:	n/a	n/a
40	POLR2A	chr4:3042174-3043956	GM12891	blood:	n/a	n/a
41	EBF1	chr4:3042931-3044004	GM12878	blood:	n/a	chr4:3043105-3043116
42	CEBPB	chr4:3043623-3043973	IMR90	lung:	n/a	n/a
43	POU2F2	chr4:3042945-3043991	GM12891	blood:	n/a	chr4:3043363-3043375 chr4:3043591-3043603
44	TCF12	chr4:3043539-3043870	GM12878	blood:	n/a	chr4:3043821-3043831
45	POLR2A	chr4:3042829-3043945	GM12892	blood:	n/a	n/a
46	RELA	chr4:3042951-3043797	GM19099	blood:	n/a	n/a
47	CHD2	chr4:3042277-3043745	GM12878	blood:	n/a	n/a
48	MAX	chr4:3042171-3043968	GM12878	blood:	n/a	chr4:3043238-3043246
49	TCF3	chr4:3042354-3043905	GM12878	blood:	n/a	chr4:3043751-3043765 chr4:3043892-3043902
50	POLR2A	chr4:3042171-3044373	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3038856..3040749-chr4:3043216..3045055,2	MCF-7	breast:
2	chr4:3038898..3040591-chr4:3042630..3044225,2	K562	blood:

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

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1008210	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1010290	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1313768	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1313771	0.82[ASN][1000 genomes]
rs1557213	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1801058	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2071688	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2071689	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2157097	0.84[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs2187694	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2187695	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2211474	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2471347	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2798286	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2798298	0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2798303	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2798304	0.81[ASN][1000 genomes]
rs2857839	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2857841	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2857852	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[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	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
rs2857849	GRK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3041800-3044400	Flanking Active TSS	Primary B cells from peripheral blood	blood
2	chr4:3042200-3044400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:3042400-3044600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:3042400-3044600	Flanking Active TSS	GM12878-XiMat	blood
5	chr4:3042600-3043800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:3042600-3044000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:3042600-3044000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:3042600-3044200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
9	chr4:3042600-3044600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:3042600-3044600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr4:3042800-3044200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr4:3042800-3044200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr4:3042800-3044200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr4:3042800-3044200	Active TSS	Brain Cingulate Gyrus	brain
15	chr4:3042800-3044200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:3042800-3044200	Active TSS	Colon Smooth Muscle	Colon
17	chr4:3042800-3044200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
18	chr4:3042800-3044200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
19	chr4:3042800-3044200	Active TSS	Left Ventricle	heart
20	chr4:3042800-3044400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:3042800-3044400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:3042800-3044400	Active TSS	Brain Anterior Caudate	brain
23	chr4:3042800-3044400	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr4:3042800-3044400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
25	chr4:3042800-3044600	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr4:3042800-3044600	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr4:3042800-3044600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr4:3043000-3043800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
29	chr4:3043000-3043800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr4:3043000-3043800	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr4:3043000-3043800	Active TSS	Placenta Amnion	Placenta Amnion
32	chr4:3043000-3043800	Flanking Active TSS	HMEC	breast
33	chr4:3043000-3044000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:3043000-3044000	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr4:3043000-3044000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:3043000-3044000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:3043000-3044000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
38	chr4:3043000-3044000	Bivalent Enhancer	Fetal Thymus	thymus
39	chr4:3043000-3044000	Active TSS	Pancreas	Pancrea
40	chr4:3043000-3044000	Active TSS	Right Ventricle	heart
41	chr4:3043000-3044000	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr4:3043000-3044000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
43	chr4:3043000-3044000	Flanking Active TSS	HUVEC	blood vessel
44	chr4:3043000-3044200	Flanking Active TSS	Liver	Liver
45	chr4:3043000-3044200	Active TSS	Brain Angular Gyrus	brain
46	chr4:3043000-3044200	Active TSS	Brain Hippocampus Middle	brain
47	chr4:3043000-3044200	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr4:3043000-3044200	Bivalent/Poised TSS	Fetal Brain Female	brain
49	chr4:3043000-3044200	Flanking Active TSS	Placenta	Placenta
50	chr4:3043000-3044200	Active TSS	Psoas Muscle	Psoas

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