Variant report

Variant	rs58688978
Chromosome Location	chr4:9693903-9693904
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	chr4:9693874-9694476	H1-hESC	embryonic stem cell:	n/a	n/a
2	PAX5	chr4:9693793-9694477	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:9692444-9693955	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOSL2	chr4:9693856-9694736	HepG2	liver:	n/a	chr4:9694539-9694548 chr4:9694540-9694549
5	POLR2A	chr4:9693836-9694629	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr4:9693805-9694461	GM12878	blood:	n/a	n/a
7	POU2F2	chr4:9693848-9694586	GM12878	blood:	n/a	n/a
8	IRF4	chr4:9693902-9694205	GM12878	blood:	n/a	n/a
9	TCF12	chr4:9693889-9694116	GM12878	blood:	n/a	n/a
10	HEY1	chr4:9693791-9694392	K562	blood:	n/a	n/a
11	PAX5	chr4:9693895-9694188	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:9693807-9694099	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
FAM86MP	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs35199477	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35352906	0.82[ASN][1000 genomes]
rs4259062	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4260536	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4362821	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4417968	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4446308	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4550924	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57402803	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs57553236	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57868742	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61031859	1.00[EUR][1000 genomes]
rs6822851	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6822895	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6827717	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6836522	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6838107	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6858190	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73802958	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73802959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7689419	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796218	chr4:9324644-9714338	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv428108	chr4:9324644-9764173	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv533218	chr4:9371016-10252290	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	74 gene(s)	inside rSNPs	diseases
4	nsv818213	chr4:9371116-9719981	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	esv2754610	chr4:9372303-9804524	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
6	nsv530090	chr4:9383695-10165033	Enhancers Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
7	nsv1012865	chr4:9429299-9794181	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1001143	chr4:9435322-9794181	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1011425	chr4:9436994-9715105	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1002981	chr4:9446035-9698645	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
11	nsv1007204	chr4:9456977-9707068	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1006867	chr4:9456977-9713612	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
13	nsv1002757	chr4:9456977-9715105	Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
14	nsv1012621	chr4:9456977-9802366	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
15	nsv1012965	chr4:9461218-9696765	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
16	nsv1012634	chr4:9461218-9802366	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
17	nsv998043	chr4:9496282-9830208	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
18	esv10795	chr4:9508396-9745703	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
19	nsv878667	chr4:9543673-9903121	ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
20	nsv878669	chr4:9551094-9794724	Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
21	nsv469511	chr4:9609987-9754029	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
22	nsv482424	chr4:9609987-9754029	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
23	nsv964031	chr4:9629449-9764955	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv1000853	chr4:9632436-9696765	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv999102	chr4:9633247-9794181	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:9692600-9694000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
2	chr4:9692600-9694000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:9692600-9694000	Active TSS	Brain Cingulate Gyrus	brain
4	chr4:9692600-9694000	Active TSS	Brain Germinal Matrix	brain
5	chr4:9692600-9694000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr4:9692600-9694200	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr4:9693000-9694000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:9693000-9694000	Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr4:9693000-9694000	Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr4:9693000-9694000	Active TSS	Stomach Smooth Muscle	stomach
11	chr4:9693400-9694000	Enhancers	Stomach Mucosa	stomach
12	chr4:9693400-9694600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:9693400-9695200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr4:9693400-9699600	Weak transcription	Spleen	Spleen
15	chr4:9693600-9694000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:9693600-9694000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:9693600-9694000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:9693600-9694000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr4:9693600-9694000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:9693600-9694000	Enhancers	Duodenum Mucosa	Duodenum
21	chr4:9693600-9694000	Enhancers	Fetal Intestine Large	intestine
22	chr4:9693600-9694000	Enhancers	Small Intestine	intestine
23	chr4:9693600-9694200	Flanking Active TSS	Thymus	Thymus
24	chr4:9693600-9694600	Enhancers	Fetal Muscle Trunk	muscle
25	chr4:9693600-9694800	Enhancers	Primary T cells fromperipheralblood	blood
26	chr4:9693600-9699600	Weak transcription	Right Ventricle	heart
27	chr4:9693800-9694000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr4:9693800-9694000	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr4:9693800-9694000	Enhancers	Adipose Nuclei	Adipose
30	chr4:9693800-9694000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:9693800-9694000	Enhancers	Colon Smooth Muscle	Colon
32	chr4:9693800-9694000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr4:9693800-9694000	Flanking Active TSS	Fetal Brain Female	brain
34	chr4:9693800-9694000	Enhancers	Fetal Intestine Small	intestine
35	chr4:9693800-9694000	Enhancers	Fetal Lung	lung
36	chr4:9693800-9694000	Enhancers	Fetal Stomach	stomach
37	chr4:9693800-9694000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr4:9693800-9694000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr4:9693800-9694000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr4:9693800-9694200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:9693800-9694200	Enhancers	Esophagus	oesophagus
42	chr4:9693800-9694400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr4:9693800-9694400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr4:9693800-9694400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr4:9693800-9694400	Enhancers	Pancreas	Pancrea
46	chr4:9693800-9694600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr4:9693800-9694600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:9693800-9694600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr4:9693800-9694800	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr4:9693800-9695000	Enhancers	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links