Variant report

Variant	rs3822444
Chromosome Location	chr5:7872150-7872151
allele	C/T
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	TCF12	chr5:7871943-7872186	GM12878	blood:	n/a	n/a
2	MXI1	chr5:7871888-7872292	GM12878	blood:	n/a	n/a
3	IKZF1	chr5:7871768-7872210	GM12878	blood:	n/a	n/a
4	CTCF	chr5:7872000-7872150	GM12872	blood:	n/a	n/a
5	NFIC	chr5:7871818-7872250	GM12878	blood:	n/a	n/a
6	CHD2	chr5:7871918-7872193	GM12878	blood:	n/a	n/a
7	CTCF	chr5:7872040-7872190	GM12864	blood:	n/a	n/a
8	ZNF384	chr5:7871951-7872311	GM12878	blood:	n/a	n/a
9	RUNX3	chr5:7871799-7872287	GM12878	blood:	n/a	n/a
10	CTCF	chr5:7872000-7872150	GM12871	blood:	n/a	n/a
11	TCF3	chr5:7871874-7872213	GM12878	blood:	n/a	chr5:7872083-7872098 chr5:7872086-7872095
12	RUNX3	chr5:7871777-7872287	GM12878	blood:	n/a	n/a
13	NR2F2	chr5:7871847-7872240	K562	blood:	n/a	n/a
14	CUX1	chr5:7871922-7872225	GM12878	blood:	n/a	chr5:7872076-7872092

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:7871956..7873701-chr5:7883684..7886400,3	K562	blood:

Variant related genes	Relation type
FASTKD3	TF binding region
MTRR	TF binding region
ENSG00000124275	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16879236	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16879248	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16879259	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16879334	0.87[AFR][1000 genomes]
rs16879342	0.87[AFR][1000 genomes]
rs2277957	0.87[AFR][1000 genomes]
rs2287779	0.87[AFR][1000 genomes]
rs2287780	0.87[AFR][1000 genomes]
rs3733781	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3756439	0.87[AFR][1000 genomes]
rs3776458	0.87[AFR][1000 genomes]
rs3776460	0.87[AFR][1000 genomes]
rs3776463	0.91[AMR][1000 genomes]
rs3776464	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs3822442	0.87[AFR][1000 genomes]
rs3822443	0.87[AFR][1000 genomes]
rs3822445	0.98[ASN][1000 genomes]
rs59809395	0.87[AFR][1000 genomes]
rs73737646	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73737647	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73737651	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916892	chr5:7634377-8158890	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv949492	chr5:7682909-7953909	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv533983	chr5:7701457-8275379	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv597005	chr5:7860404-8093077	Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv427707	chr5:7866234-7966019	Strong transcription Active TSS Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:7870000-7873000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:7870000-7875400	Weak transcription	Spleen	Spleen
3	chr5:7870200-7873400	Flanking Active TSS	GM12878-XiMat	blood
4	chr5:7870200-7875400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr5:7870200-7875600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:7870200-7875600	Weak transcription	HSMMtube	muscle
7	chr5:7870200-7875800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:7870200-7875800	Weak transcription	Esophagus	oesophagus
9	chr5:7870200-7875800	Weak transcription	Gastric	stomach
10	chr5:7870200-7876000	Weak transcription	Fetal Brain Male	brain
11	chr5:7870200-7879800	Weak transcription	Pancreas	Pancrea
12	chr5:7870200-7882000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:7870200-7903400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:7870400-7872200	Enhancers	Stomach Mucosa	stomach
15	chr5:7870400-7872600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:7870400-7873200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr5:7870400-7873600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr5:7870400-7874400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr5:7870400-7875400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr5:7870400-7875600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr5:7870400-7875600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr5:7870600-7873000	Genic enhancers	HSMM	muscle
23	chr5:7870600-7874800	Weak transcription	Fetal Kidney	kidney
24	chr5:7870600-7876200	Weak transcription	Fetal Stomach	stomach
25	chr5:7870600-7878000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:7870600-7878400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr5:7870800-7872200	Enhancers	HepG2	liver
28	chr5:7870800-7872800	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr5:7870800-7872800	Enhancers	Duodenum Mucosa	Duodenum
30	chr5:7870800-7873200	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr5:7870800-7875400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr5:7870800-7875600	Weak transcription	Fetal Brain Female	brain
33	chr5:7870800-7879800	Weak transcription	Colonic Mucosa	Colon
34	chr5:7871000-7872400	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr5:7871000-7872800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:7871000-7873000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr5:7871000-7873000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr5:7871000-7873000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:7871000-7873000	Weak transcription	Fetal Lung	lung
40	chr5:7871000-7873000	Weak transcription	Thymus	Thymus
41	chr5:7871000-7873400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:7871000-7874000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr5:7871000-7874000	Weak transcription	NHDF-Ad	bronchial
44	chr5:7871000-7874600	Weak transcription	Adipose Nuclei	Adipose
45	chr5:7871000-7875400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:7871000-7875400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:7871000-7875400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr5:7871000-7875400	Weak transcription	HUVEC	blood vessel
49	chr5:7871000-7875400	Weak transcription	NH-A	brain
50	chr5:7871000-7875400	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links