Variant report

Variant	rs60652723
Chromosome Location	chr2:47169876-47169877
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	RELA	chr2:47168667-47169932	GM19193	blood:	n/a	n/a
2	POLR2A	chr2:47169845-47169927	GM12878	blood:	n/a	n/a
3	TBP	chr2:47168783-47169900	GM12878	blood:	n/a	n/a
4	RUNX3	chr2:47168562-47169995	GM12878	blood:	n/a	chr2:47169041-47169056
5	RCOR1	chr2:47168573-47169909	GM12878	blood:	n/a	n/a
6	WRNIP1	chr2:47169657-47169937	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:47167963-47169919	GM12892	blood:	n/a	n/a
8	IRF4	chr2:47169218-47169888	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:47168094-47171520	GM12878	blood:	n/a	n/a
10	BCLAF1	chr2:47169130-47169913	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:47168234-47169908	GM12878	blood:	n/a	n/a
12	TBL1XR1	chr2:47168676-47169909	GM12878	blood:	n/a	n/a
13	FOXM1	chr2:47168621-47169895	GM12878	blood:	n/a	n/a
14	NFIC	chr2:47168980-47170017	GM12878	blood:	n/a	n/a
15	RELA	chr2:47168253-47169893	GM10847	blood:	n/a	n/a
16	POLR2A	chr2:47168084-47171676	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:47169638-47169966	GM12892	blood:	n/a	n/a
18	MAZ	chr2:47166483-47170044	IMR90	lung:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47166847-47166856 chr2:47167751-47167760
19	POLR2A	chr2:47168238-47171702	GM12891	blood:	n/a	n/a
20	RELA	chr2:47168645-47169947	GM19099	blood:	n/a	n/a
21	MAX	chr2:47166973-47170077	A549	lung:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47167751-47167760
22	RELA	chr2:47168062-47171777	GM12891	blood:	n/a	n/a
23	RELA	chr2:47168206-47169976	GM15510	blood:	n/a	n/a
24	POLR2A	chr2:47168067-47169925	GM12878	blood:	n/a	n/a
25	BCL3	chr2:47169356-47170020	A549	lung:	n/a	n/a
26	MAZ	chr2:47167889-47169919	GM12878	blood:	n/a	chr2:47168106-47168116 chr2:47169037-47169048
27	PML	chr2:47168528-47169957	GM12878	blood:	n/a	n/a
28	MTA3	chr2:47168787-47169941	GM12878	blood:	n/a	n/a
29	STAT1	chr2:47168934-47169882	GM12878	blood:	n/a	n/a
30	POLR2A	chr2:47168586-47171994	GM12878	blood:	n/a	n/a
31	STAT5A	chr2:47168585-47170045	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:47167902-47170112	GM18951	blood:	n/a	n/a
33	POLR2A	chr2:47167794-47169992	GM19099	blood:	n/a	n/a
34	POLR2A	chr2:47169729-47170006	HepG2	liver:	n/a	n/a
35	MTA3	chr2:47168504-47170041	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47145255..47147590-chr2:47169697..47171236,2	K562	blood:
2	chr2:47166915..47170495-chr2:47399445..47404516,7	MCF-7	breast:
3	chr2:47139463..47143529-chr2:47167839..47169953,4	K562	blood:
4	chr2:47135393..47141252-chr2:47166022..47170880,5	K562	blood:
5	chr2:47168040..47171171-chr2:47402063..47404163,4	K562	blood:
6	chr2:47165446..47170208-chr2:47173646..47177856,9	MCF-7	breast:
7	chr2:47169747..47171383-chr2:47233270..47235359,2	MCF-7	breast:
8	chr2:47143277..47146895-chr2:47166934..47170660,7	MCF-7	breast:
9	chr2:47167291..47170086-chr2:47204793..47207048,4	MCF-7	breast:
10	chr2:47139886..47146981-chr2:47165365..47170438,17	MCF-7	breast:
11	chr2:47168340..47172583-chr2:47183123..47189203,6	MCF-7	breast:
12	chr2:47166107..47171055-chr2:47402078..47404965,9	K562	blood:

Variant related genes	Relation type
MCFD2	TF binding region
ENSG00000068724	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000272814	Chromatin interaction
ENSG00000180398	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10495940	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55654964	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60630351	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61616404	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6717185	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6741399	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6759170	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72886646	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72886669	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886689	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7556761	0.87[AFR][1000 genomes]
rs7570279	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47167600-47170000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:47167600-47170400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:47167600-47170400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:47167600-47170400	Active TSS	Rectal Smooth Muscle	rectum
5	chr2:47167600-47170600	Active TSS	Thymus	Thymus
6	chr2:47167800-47170000	Active TSS	Esophagus	oesophagus
7	chr2:47167800-47170000	Active TSS	Spleen	Spleen
8	chr2:47167800-47170400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:47168000-47170400	Active TSS	GM12878-XiMat	blood
10	chr2:47168000-47170400	Active TSS	HSMM	muscle
11	chr2:47168000-47170400	Active TSS	NHDF-Ad	bronchial
12	chr2:47168000-47170400	Active TSS	NHLF	lung
13	chr2:47168200-47170200	Active TSS	Colonic Mucosa	Colon
14	chr2:47168600-47170000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr2:47168600-47170000	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr2:47168600-47170200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:47168600-47171000	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr2:47168600-47171400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:47168800-47170200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr2:47169000-47170000	Flanking Active TSS	HUVEC	blood vessel
21	chr2:47169000-47170000	Flanking Active TSS	K562	blood
22	chr2:47169000-47170200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr2:47169000-47170400	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr2:47169000-47170600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:47169000-47170800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:47169000-47171200	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr2:47169000-47171400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr2:47169000-47171400	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr2:47169000-47171600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr2:47169200-47170000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
31	chr2:47169200-47170000	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr2:47169200-47170000	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr2:47169200-47170000	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr2:47169200-47170000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr2:47169200-47170000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:47169200-47170000	Flanking Active TSS	NH-A	brain
37	chr2:47169200-47170200	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr2:47169200-47170200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr2:47169200-47170600	Flanking Active TSS	Dnd41	blood
40	chr2:47169400-47170000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
41	chr2:47169400-47170000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:47169400-47170000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:47169400-47170000	Flanking Active TSS	Fetal Intestine Large	intestine
44	chr2:47169400-47170000	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr2:47169400-47170000	Active TSS	Psoas Muscle	Psoas
46	chr2:47169400-47170000	Active TSS	Right Atrium	heart
47	chr2:47169400-47170000	Active TSS	HSMMtube	muscle
48	chr2:47169400-47170200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:47169400-47171200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr2:47169400-47171200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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