Variant report

Variant	rs34261027
Chromosome Location	chr3:52490391-52490392
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr3:52489193-52490991	H1-neurons	neurons:	n/a	n/a
2	CTCF	chr3:52490360-52490510	HRE	kidney:	n/a	n/a
3	ZBTB7A	chr3:52489307-52490753	ECC-1	luminal epithelium:	n/a	chr3:52489757-52489766
4	POLR2A	chr3:52490179-52490853	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZNF263	chr3:52490208-52491056	HEK293-T-REx	kidney:	n/a	chr3:52490582-52490591
6	ZBTB7A	chr3:52489116-52490504	ECC-1	luminal epithelium:	n/a	chr3:52489757-52489766
7	POLR2A	chr3:52490272-52490850	K562	blood:	n/a	n/a
8	POLR2A	chr3:52490064-52490818	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr3:52490061-52490596	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr3:52490028-52490985	H1-neurons	neurons:	n/a	n/a
11	HCFC1	chr3:52488514-52490426	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr3:52488611-52491002	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr3:52489121-52491062	HUVEC	blood vessel:	n/a	n/a
14	TAF1	chr3:52490043-52490610	H1-hESC	embryonic stem cell:	n/a	n/a
15	SIN3A	chr3:52489275-52490759	H1-hESC	embryonic stem cell:	n/a	n/a
16	MXI1	chr3:52489139-52491119	IMR90	lung:	n/a	n/a
17	REST	chr3:52488954-52491144	H1-neurons	neurons:	n/a	n/a
18	MAZ	chr3:52489179-52490898	IMR90	lung:	n/a	chr3:52489875-52489885
19	CHD1	chr3:52490139-52490409	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:52490155-52490875	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr3:52487592-52491009	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:52490321-52490709	SK-N-SH	brain:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52486786..52490623-chr3:52738506..52740742,3	MCF-7	breast:
2	chr3:52487939..52491238-chr3:52504089..52507877,6	MCF-7	breast:
3	chr3:52489123..52491255-chr3:52558992..52560564,2	MCF-7	breast:
4	chr3:52488362..52490407-chr3:52528579..52530282,2	K562	blood:
5	chr3:52487897..52490713-chr3:52565636..52568320,3	K562	blood:
6	chr3:52488681..52492997-chr3:52505692..52511376,6	K562	blood:
7	chr3:52488315..52491899-chr3:52569459..52572680,4	MCF-7	breast:
8	chr3:52487997..52491865-chr3:52718755..52722667,5	MCF-7	breast:
9	chr3:52489605..52491332-chr3:52564945..52566721,2	K562	blood:
10	chr3:52488081..52492441-chr3:52568649..52570860,4	K562	blood:
11	chr3:52444497..52446102-chr3:52488760..52490756,2	K562	blood:
12	chr3:52457971..52460550-chr3:52489642..52491148,2	K562	blood:
13	chr3:52490212..52491828-chr3:52494958..52496953,2	K562	blood:

No data

Variant related genes	Relation type
TNNC1	TF binding region
NISCH	TF binding region
ENSG00000010318	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000010327	Chromatin interaction
ENSG00000168273	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1011063	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1077142	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10865972	0.90[ASN][1000 genomes]
rs11705963	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11706108	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11707864	0.80[EUR][1000 genomes]
rs11709658	0.80[EUR][1000 genomes]
rs11714402	0.84[EUR][1000 genomes]
rs11716017	0.80[EUR][1000 genomes]
rs11718125	0.83[EUR][1000 genomes]
rs11721286	1.00[ASN][1000 genomes]
rs123602	0.87[EUR][1000 genomes]
rs13059674	0.84[EUR][1000 genomes]
rs13075370	0.80[EUR][1000 genomes]
rs13076890	0.84[EUR][1000 genomes]
rs13091545	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1541495	1.00[ASN][1000 genomes]
rs17052058	0.81[EUR][1000 genomes]
rs17052061	0.81[EUR][1000 genomes]
rs2016575	0.91[EUR][1000 genomes]
rs2109558	1.00[ASN][1000 genomes]
rs2109559	1.00[ASN][1000 genomes]
rs2159607	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2335640	0.81[EUR][1000 genomes]
rs28481563	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34238085	0.84[EUR][1000 genomes]
rs34355561	0.80[EUR][1000 genomes]
rs34523877	0.84[EUR][1000 genomes]
rs34762015	0.81[EUR][1000 genomes]
rs34908451	0.81[EUR][1000 genomes]
rs35860312	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3752819	0.80[EUR][1000 genomes]
rs390802	0.86[EUR][1000 genomes]
rs4687543	0.83[ASN][1000 genomes]
rs4687617	1.00[ASN][1000 genomes]
rs498946	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55965068	0.82[EUR][1000 genomes]
rs55997317	0.82[EUR][1000 genomes]
rs57441156	0.82[EUR][1000 genomes]
rs59612757	0.81[EUR][1000 genomes]
rs634382	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6445386	0.82[EUR][1000 genomes]
rs6445506	1.00[ASN][1000 genomes]
rs66462821	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67248391	0.81[EUR][1000 genomes]
rs67834575	0.81[EUR][1000 genomes]
rs6784615	1.00[ASN][1000 genomes]
rs6794675	0.84[EUR][1000 genomes]
rs6796333	0.80[EUR][1000 genomes]
rs6800707	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728408	1.00[ASN][1000 genomes]
rs7620015	1.00[ASN][1000 genomes]
rs7643570	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs82825	0.90[EUR][1000 genomes]
rs887514	1.00[ASN][1000 genomes]
rs887515	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844183	0.80[EUR][1000 genomes]
rs9861879	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv876794	chr3:52485876-52496229	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52488600-52490600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:52488800-52491800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:52489000-52490800	Active TSS	Aorta	Aorta
4	chr3:52489000-52490800	Active TSS	Fetal Kidney	kidney
5	chr3:52489000-52490800	Active TSS	Ovary	ovary
6	chr3:52489000-52491200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr3:52489200-52490400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:52489200-52490400	Active TSS	Brain Hippocampus Middle	brain
9	chr3:52489200-52490600	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr3:52489200-52490600	Active TSS	Gastric	stomach
11	chr3:52489200-52490600	Active TSS	Left Ventricle	heart
12	chr3:52489200-52490600	Active TSS	Lung	lung
13	chr3:52489200-52490600	Active TSS	Psoas Muscle	Psoas
14	chr3:52489200-52490600	Active TSS	A549	lung
15	chr3:52489200-52490800	Active TSS	Right Atrium	heart
16	chr3:52489200-52491000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:52489400-52490400	Active TSS	H1 Cell Line	embryonic stem cell
18	chr3:52489400-52490400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:52489400-52490400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:52489400-52490400	Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr3:52489400-52490400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:52489400-52490400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
23	chr3:52489400-52490400	Active TSS	Brain Substantia Nigra	brain
24	chr3:52489400-52490400	Active TSS	Colon Smooth Muscle	Colon
25	chr3:52489400-52490400	Active TSS	Fetal Intestine Large	intestine
26	chr3:52489400-52490400	Active TSS	Fetal Muscle Leg	muscle
27	chr3:52489400-52490400	Active TSS	Placenta	Placenta
28	chr3:52489400-52490400	Active TSS	Fetal Thymus	thymus
29	chr3:52489400-52490400	Active TSS	Dnd41	blood
30	chr3:52489400-52490400	Active TSS	HUVEC	blood vessel
31	chr3:52489400-52490400	Active TSS	NHEK	skin
32	chr3:52489400-52490400	Active TSS	Osteobl	bone
33	chr3:52489400-52490600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:52489400-52490600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:52489400-52490600	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr3:52489400-52490600	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr3:52489400-52490600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:52489400-52490600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:52489400-52490600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:52489400-52490600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:52489400-52490600	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr3:52489400-52490600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:52489400-52490600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:52489400-52490600	Active TSS	Fetal Intestine Small	intestine
45	chr3:52489400-52490600	Active TSS	Fetal Lung	lung
46	chr3:52489400-52490600	Active TSS	Fetal Stomach	stomach
47	chr3:52489400-52490600	Active TSS	Placenta Amnion	Placenta Amnion
48	chr3:52489400-52490600	Active TSS	Rectal Smooth Muscle	rectum
49	chr3:52489400-52490600	Active TSS	NH-A	brain
50	chr3:52489400-52490600	Active TSS	NHLF	lung

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