Variant report

Variant	rs28559768
Chromosome Location	chr7:99846454-99846455
allele	A/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	POLR2A	chr7:99846379-99846707	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99844918..99846658-chr7:99861769..99864301,2	K562	blood:
2	chr7:99754140..99756334-chr7:99844492..99846727,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239521	TF binding region
ENSG00000146826	Chromatin interaction
ENSG00000266154	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10224352	0.93[AFR][1000 genomes]
rs10225636	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10245781	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10245955	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10257359	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10261440	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10268724	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10269973	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57116449	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60568054	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
2	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers 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	1085 gene(s)	inside rSNPs	diseases
3	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
4	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
5	nsv427794	chr7:99750981-99960900	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
6	nsv428180	chr7:99750981-99960900	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Genic enhancers 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 miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv8182	chr7:99799816-99879781	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv888774	chr7:99807265-99951315	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	esv16057	chr7:99809377-99937347	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	esv3379367	chr7:99811760-99938687	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	esv3379649	chr7:99812207-99939196	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
13	esv3358931	chr7:99816130-99943645	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	esv3405423	chr7:99816156-99943860	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
15	esv3508070	chr7:99816206-99943813	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
16	esv3508071	chr7:99816206-99943813	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
17	nsv981558	chr7:99836239-99870051	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99807200-99847000	Weak transcription	Fetal Kidney	kidney
2	chr7:99810600-99864000	Weak transcription	Right Atrium	heart
3	chr7:99813800-99846800	Weak transcription	Ovary	ovary
4	chr7:99821600-99867800	Weak transcription	Gastric	stomach
5	chr7:99823200-99862600	Weak transcription	Spleen	Spleen
6	chr7:99823800-99864200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr7:99829200-99860600	Weak transcription	Dnd41	blood
8	chr7:99831400-99864200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:99831800-99853000	Weak transcription	Fetal Brain Female	brain
10	chr7:99833000-99868600	Weak transcription	Primary T cells from cord blood	blood
11	chr7:99833200-99868600	Weak transcription	Thymus	Thymus
12	chr7:99840200-99863600	Weak transcription	Brain Anterior Caudate	brain
13	chr7:99841400-99847000	Enhancers	Fetal Muscle Leg	muscle
14	chr7:99841400-99864000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr7:99842000-99868400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr7:99842800-99858200	Weak transcription	Brain Substantia Nigra	brain
17	chr7:99844000-99847200	Enhancers	H1 Cell Line	embryonic stem cell
18	chr7:99844400-99846600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr7:99844800-99846600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:99845200-99868200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr7:99845400-99853800	Weak transcription	Fetal Stomach	stomach
22	chr7:99845400-99858200	Weak transcription	Fetal Intestine Small	intestine
23	chr7:99845400-99860400	Weak transcription	Fetal Intestine Large	intestine
24	chr7:99845400-99863800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:99845400-99868200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:99845600-99847400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr7:99845800-99847000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr7:99846000-99846600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr7:99846000-99847000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:99846000-99847200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr7:99846000-99847200	Enhancers	Psoas Muscle	Psoas
32	chr7:99846200-99846600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:99846200-99846600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr7:99846200-99847200	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr7:99846200-99860400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:99846200-99867200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr7:99846200-99867400	Weak transcription	Fetal Thymus	thymus
38	chr7:99846400-99846800	Weak transcription	Stomach Mucosa	stomach
39	chr7:99846400-99847000	Weak transcription	Brain Angular Gyrus	brain
40	chr7:99846400-99847000	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr7:99846400-99847200	Enhancers	A549	lung
42	chr7:99846400-99847200	Enhancers	Hela-S3	cervix
43	chr7:99846400-99848000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr7:99846400-99850200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr7:99846400-99852400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr7:99846400-99861200	Weak transcription	Brain Germinal Matrix	brain
47	chr7:99846400-99861600	Weak transcription	Brain Hippocampus Middle	brain
48	chr7:99846400-99863400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr7:99846400-99866800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr7:99846400-99867000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links