Variant report

Variant	rs3130244
Chromosome Location	chr6:30552937-30552938
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30552828-30553214	GM12891	blood:	n/a	n/a
2	POLR2A	chr6:30552846-30553577	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:30552860-30553440	K562	blood:	n/a	n/a
4	POLR2A	chr6:30552704-30552954	K562	blood:	n/a	n/a
5	POLR2A	chr6:30552071-30553527	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:30552470-30553280	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:30552581-30553288	K562	blood:	n/a	n/a
8	POLR2A	chr6:30552546-30553897	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30522844..30526693-chr6:30552290..30555314,4	MCF-7	breast:
2	chr6:30550158..30553147-chr6:30570256..30572566,2	MCF-7	breast:
3	chr6:30547585..30549904-chr6:30552603..30554417,2	MCF-7	breast:
4	chr6:30524314..30526715-chr6:30551003..30553176,2	MCF-7	breast:

No data

Variant related genes	Relation type
ABCF1	TF binding region
ENSG00000204576	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000204590	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1058318	0.85[EUR][1000 genomes]
rs1264432	0.81[EUR][1000 genomes]
rs1264437	0.84[EUR][1000 genomes]
rs1264438	0.84[EUR][1000 genomes]
rs1264439	0.83[EUR][1000 genomes]
rs1264440	0.92[EUR][1000 genomes]
rs1264448	0.83[EUR][1000 genomes]
rs1362119	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1468079	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2023608	0.88[EUR][1000 genomes]
rs2023609	0.88[EUR][1000 genomes]
rs2074503	0.85[EUR][1000 genomes]
rs2074504	0.82[EUR][1000 genomes]
rs2074505	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2269709	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2269710	0.88[EUR][1000 genomes]
rs2429655	0.88[EUR][1000 genomes]
rs2429656	0.81[EUR][1000 genomes]
rs2508021	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2508024	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2516639	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2516641	0.85[EUR][1000 genomes]
rs2516642	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2516643	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2516644	0.91[EUR][1000 genomes]
rs2516646	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2516647	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2516648	0.88[EUR][1000 genomes]
rs2516649	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2516653	0.82[EUR][1000 genomes]
rs2516655	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2516656	0.88[EUR][1000 genomes]
rs2516662	0.88[EUR][1000 genomes]
rs2524221	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2524223	0.84[EUR][1000 genomes]
rs2524224	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2524225	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2524226	0.84[EUR][1000 genomes]
rs2534802	0.87[EUR][1000 genomes]
rs2534806	0.81[EUR][1000 genomes]
rs2534807	0.88[EUR][1000 genomes]
rs2534808	0.81[EUR][1000 genomes]
rs2534809	0.83[EUR][1000 genomes]
rs2534810	0.87[EUR][1000 genomes]
rs2534811	0.80[AMR][1000 genomes]
rs2534812	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2534813	0.88[EUR][1000 genomes]
rs2534814	0.81[EUR][1000 genomes]
rs2534815	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2534821	0.82[EUR][1000 genomes]
rs2534823	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2534824	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2534825	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2844713	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2844714	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2844715	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2844716	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2844717	0.88[EUR][1000 genomes]
rs2844718	0.88[EUR][1000 genomes]
rs2844720	0.88[EUR][1000 genomes]
rs2844723	0.87[EUR][1000 genomes]
rs2844724	0.88[EUR][1000 genomes]
rs2844725	0.83[EUR][1000 genomes]
rs3094718	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3130039	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3130041	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3130043	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3130045	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3130240	0.89[EUR][1000 genomes]
rs3130242	0.85[EUR][1000 genomes]
rs3130243	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3132609	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3132612	0.81[EUR][1000 genomes]
rs3132613	0.85[EUR][1000 genomes]
rs3132614	0.86[EUR][1000 genomes]
rs9262070	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9262082	0.88[EUR][1000 genomes]
rs9262118	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs975195	0.88[EUR][1000 genomes]
rs996588	0.88[EUR][1000 genomes]
rs996589	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer 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	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
6	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
7	nsv884091	chr6:30526026-30590646	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	776 gene(s)	inside rSNPs	diseases
8	nsv5244	chr6:30545111-30589803	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	772 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	chr6:30540200-30582200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:30540200-30582200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:30540400-30563000	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr6:30540800-30560800	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr6:30540800-30563600	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:30540800-30563600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:30540800-30563800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:30541400-30567400	Weak transcription	Fetal Heart	heart
9	chr6:30541600-30555400	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:30541600-30563000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr6:30541800-30558000	Strong transcription	NHLF	lung
12	chr6:30541800-30562800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:30541800-30565200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:30542000-30562800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:30542200-30554800	Strong transcription	Primary B cells from cord blood	blood
16	chr6:30542200-30555000	Strong transcription	NHEK	skin
17	chr6:30542200-30556800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:30542200-30557800	Strong transcription	Placenta	Placenta
19	chr6:30542200-30563200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:30542200-30564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:30542200-30581800	Weak transcription	Right Atrium	heart
22	chr6:30542600-30558400	Strong transcription	Fetal Thymus	thymus
23	chr6:30542800-30563400	Strong transcription	Fetal Stomach	stomach
24	chr6:30543000-30562800	Strong transcription	Thymus	Thymus
25	chr6:30543200-30554000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:30543200-30555000	Strong transcription	NHDF-Ad	bronchial
27	chr6:30543200-30555200	Strong transcription	Left Ventricle	heart
28	chr6:30543200-30557200	Strong transcription	Fetal Lung	lung
29	chr6:30543200-30557600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:30543200-30557800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:30543200-30557800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:30543200-30558000	Strong transcription	Lung	lung
33	chr6:30543200-30558000	Strong transcription	Osteobl	bone
34	chr6:30543200-30558200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:30543200-30560400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr6:30543200-30562800	Strong transcription	Adipose Nuclei	Adipose
37	chr6:30543200-30563000	Strong transcription	Fetal Brain Female	brain
38	chr6:30543200-30563000	Strong transcription	Fetal Muscle Trunk	muscle
39	chr6:30543200-30563000	Strong transcription	Fetal Muscle Leg	muscle
40	chr6:30543200-30563400	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr6:30543200-30563400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:30543200-30563600	Strong transcription	Stomach Smooth Muscle	stomach
43	chr6:30543400-30555000	Strong transcription	K562	blood
44	chr6:30543400-30557400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:30543400-30560600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr6:30543400-30560800	Strong transcription	Brain Hippocampus Middle	brain
47	chr6:30543400-30563000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:30543400-30563000	Strong transcription	Primary T cells from cord blood	blood
49	chr6:30543400-30563000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:30543400-30563400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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