Variant report

Variant	rs13220225
Chromosome Location	chr6:30747802-30747803
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr6:30747730-30748275	T-47D	breast:	n/a	n/a
2	CHD1	chr6:30746278-30750816	IMR90	lung:	n/a	n/a
3	ESR1	chr6:30747790-30748210	T-47D	breast:	n/a	n/a
4	FOS	chr6:30747759-30747866	MCF10A-Er-Src	breast:	n/a	n/a
5	ESR1	chr6:30747762-30748303	T-47D	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30745917..30748118-chr6:30776110..30778177,2	K562	blood:
2	chr6:30742016..30748001-chr6:30748066..30750476,5	MCF-7	breast:
3	chr6:30746239..30748056-chr6:30850531..30852565,3	MCF-7	breast:
4	chr6:30719384..30720067-chr6:30747678..30748455,3	MCF-7	breast:
5	chr6:30710424..30713995-chr6:30746295..30752430,9	K562	blood:

No data

Variant related genes	Relation type
HCG20	TF binding region
ENSG00000228022	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137312	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12526186	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12527188	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12660860	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12660883	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12662149	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13202739	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13214831	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13217914	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17189441	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17481190	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28670020	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28780111	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28780113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28780114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28780120	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28780121	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28780122	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28894082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3869075	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4278006	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4713361	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
9	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
10	nsv870418	chr6:30713196-30755668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv527226	chr6:30716719-30772378	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv884103	chr6:30729487-30755668	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv884104	chr6:30740680-30753146	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13220225	ZNF192	cis	cerebellum	SCAN
rs13220225	DDR1	cis	lymphoblastoid	seeQTL
rs13220225	IP6K3	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30737600-30749200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:30738600-30749200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr6:30741000-30749600	Weak transcription	Thymus	Thymus
4	chr6:30742000-30749000	Enhancers	HepG2	liver
5	chr6:30744000-30758000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr6:30744200-30748000	Enhancers	Fetal Intestine Small	intestine
7	chr6:30744200-30749200	Enhancers	Fetal Heart	heart
8	chr6:30744200-30749200	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr6:30744400-30748200	Enhancers	Primary T cells from cord blood	blood
10	chr6:30744400-30748400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr6:30744600-30748600	Enhancers	Fetal Thymus	thymus
12	chr6:30744800-30749400	Enhancers	Stomach Mucosa	stomach
13	chr6:30745000-30748400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:30745400-30749600	Enhancers	Fetal Muscle Leg	muscle
15	chr6:30745600-30749400	Enhancers	Fetal Muscle Trunk	muscle
16	chr6:30745800-30749000	Enhancers	NHDF-Ad	bronchial
17	chr6:30745800-30749200	Enhancers	NH-A	brain
18	chr6:30746000-30748200	Enhancers	K562	blood
19	chr6:30746000-30748400	Enhancers	Ovary	ovary
20	chr6:30746000-30748600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:30746000-30749200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:30746000-30749200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:30746000-30749200	Enhancers	Right Atrium	heart
24	chr6:30746000-30749200	Enhancers	Osteobl	bone
25	chr6:30746000-30749400	Enhancers	Lung	lung
26	chr6:30746000-30749800	Enhancers	Pancreas	Pancrea
27	chr6:30746000-30750000	Enhancers	Left Ventricle	heart
28	chr6:30746000-30750400	Enhancers	Fetal Stomach	stomach
29	chr6:30746000-30750400	Enhancers	Spleen	Spleen
30	chr6:30746000-30750800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr6:30746000-30750800	Enhancers	Placenta Amnion	Placenta Amnion
32	chr6:30746000-30751000	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr6:30746000-30752400	Enhancers	Placenta	Placenta
34	chr6:30746200-30748000	Enhancers	HSMM	muscle
35	chr6:30746200-30749200	Enhancers	Colonic Mucosa	Colon
36	chr6:30746200-30749200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:30746200-30749400	Weak transcription	Dnd41	blood
38	chr6:30746200-30751400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:30746400-30748800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr6:30746400-30749000	Weak transcription	Small Intestine	intestine
41	chr6:30746400-30749200	Enhancers	A549	lung
42	chr6:30746600-30749400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr6:30746600-30750400	Enhancers	Aorta	Aorta
44	chr6:30746600-30751000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr6:30746800-30749200	Enhancers	NHEK	skin
46	chr6:30746800-30751200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:30747000-30748000	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr6:30747000-30749000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:30747000-30749200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr6:30747000-30749200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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