Variant report

Variant	rs28780111
Chromosome Location	chr6:30720311-30720312
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30718958..30721409-chr6:30812435..30814738,2	MCF-7	breast:
2	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
3	chr6:30719980..30722525-chr6:30838687..30841079,2	K562	blood:
4	chr6:30718989..30721292-chr6:30772340..30774126,2	MCF-7	breast:
5	chr6:30717879..30721732-chr6:30850020..30854415,6	MCF-7	breast:
6	chr6:30719312..30720395-chr6:30766753..30767647,3	MCF-7	breast:
7	chr6:30719389..30720481-chr6:30850176..30850986,3	MCF-7	breast:
8	chr6:30719096..30721371-chr6:30880176..30882987,2	MCF-7	breast:
9	chr6:30582929..30584442-chr6:30719017..30721240,2	MCF-7	breast:
10	chr6:30720149..30720893-chr6:30781568..30782338,2	MCF-7	breast:
11	chr6:30719971..30720527-chr6:30749537..30750469,2	Hela-S3	cervix:
12	chr1:149858963..149859630-chr6:30720097..30720859,2	Hela-S3	cervix:
13	chr6:30704403..30722478-chr6:30842859..30858629,100	MCF-7	breast:
14	chr6:30703055..30723531-chr6:30783853..30800217,151	MCF-7	breast:
15	chr6:30712290..30712798-chr6:30719940..30720919,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000214894	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000228022	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000204580	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12526186	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12527188	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12660860	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12660883	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12662149	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13202739	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13214831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13217914	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13220225	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17189441	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17481190	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28670020	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28780113	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28780114	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28780120	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28780121	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28780122	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28894082	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3869075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4278006	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4713361	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	nsv884101	chr6:30695920-30733121	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	163 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv884102	chr6:30706013-30720567	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases
13	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
14	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28780111	IP6K3	cis	parietal	SCAN
rs28780111	DDR1	cis	lymphoblastoid	seeQTL
rs28780111	ZNF192	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30712600-30724000	Enhancers	HMEC	breast
2	chr6:30714200-30721200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:30715200-30720800	Enhancers	Fetal Intestine Large	intestine
4	chr6:30715200-30722200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:30715600-30721600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:30716600-30721400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr6:30717000-30724000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:30717200-30720600	Weak transcription	Aorta	Aorta
9	chr6:30717200-30721400	Enhancers	HUVEC	blood vessel
10	chr6:30717800-30721200	Enhancers	Stomach Mucosa	stomach
11	chr6:30717800-30725400	Weak transcription	Spleen	Spleen
12	chr6:30717800-30726800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:30718400-30720800	Enhancers	HepG2	liver
14	chr6:30718600-30723600	Weak transcription	Liver	Liver
15	chr6:30719000-30720600	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr6:30719000-30721200	Enhancers	Fetal Muscle Leg	muscle
17	chr6:30719200-30720600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:30719200-30720600	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr6:30719200-30721000	Enhancers	Fetal Muscle Trunk	muscle
20	chr6:30719200-30721000	Enhancers	K562	blood
21	chr6:30719200-30721200	Enhancers	Adipose Nuclei	Adipose
22	chr6:30719200-30721200	Enhancers	Placenta	Placenta
23	chr6:30719200-30721200	Enhancers	Left Ventricle	heart
24	chr6:30719200-30721400	Enhancers	Fetal Heart	heart
25	chr6:30719200-30721600	Enhancers	Colon Smooth Muscle	Colon
26	chr6:30719400-30720400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr6:30719400-30720400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:30719400-30720800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:30719400-30720800	Enhancers	Brain Anterior Caudate	brain
30	chr6:30719400-30720800	Enhancers	Esophagus	oesophagus
31	chr6:30719400-30720800	Enhancers	Fetal Lung	lung
32	chr6:30719400-30720800	Enhancers	Lung	lung
33	chr6:30719400-30720800	Enhancers	Pancreas	Pancrea
34	chr6:30719400-30721000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr6:30719400-30721200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:30719400-30721200	Enhancers	Psoas Muscle	Psoas
37	chr6:30719400-30721200	Enhancers	Right Ventricle	heart
38	chr6:30719400-30721400	Enhancers	Fetal Stomach	stomach
39	chr6:30719600-30720800	Enhancers	Brain Substantia Nigra	brain
40	chr6:30719600-30721000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:30719600-30721200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr6:30719600-30721200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:30719600-30725000	Weak transcription	GM12878-XiMat	blood
44	chr6:30719800-30720400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr6:30719800-30720400	Enhancers	NHEK	skin
46	chr6:30719800-30720600	Enhancers	Fetal Thymus	thymus
47	chr6:30719800-30721000	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr6:30719800-30721000	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr6:30719800-30721200	Enhancers	Brain Hippocampus Middle	brain
50	chr6:30719800-30721200	Enhancers	Small Intestine	intestine

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