Variant report

Variant	rs41438647
Chromosome Location	chr2:64368658-64368659
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	NFIC	chr2:64368529-64369200	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:64368621-64369212	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64368361..64371459-chr2:64452988..64456076,3	K562	blood:

Variant related genes	Relation type
ENSG00000225889	TF binding region
ENSG00000225889	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs17028475	0.96[AFR][1000 genomes]
rs17028480	0.98[AFR][1000 genomes]
rs17028484	0.98[AFR][1000 genomes]
rs17028499	0.98[AFR][1000 genomes]
rs17028503	0.98[AFR][1000 genomes]
rs17028507	0.83[AFR][1000 genomes]
rs17028510	0.98[AFR][1000 genomes]
rs17028513	0.98[AFR][1000 genomes]
rs17039958	0.98[AFR][1000 genomes]
rs41322849	0.98[AFR][1000 genomes]
rs60643329	0.98[AFR][1000 genomes]
rs72893140	0.98[AFR][1000 genomes]
rs72893145	0.98[AFR][1000 genomes]
rs72893152	0.98[AFR][1000 genomes]
rs72893157	0.98[AFR][1000 genomes]
rs72893160	0.98[AFR][1000 genomes]
rs72893162	0.98[AFR][1000 genomes]
rs72893165	0.91[AFR][1000 genomes]
rs72893168	0.83[AFR][1000 genomes]
rs72893170	0.98[AFR][1000 genomes]
rs72893172	0.98[AFR][1000 genomes]
rs72893173	0.98[AFR][1000 genomes]
rs72893175	0.98[AFR][1000 genomes]
rs72893180	0.98[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34698	chr2:64312142-64521366	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv34955	chr2:64312182-64521290	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv834243	chr2:64316514-64476935	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv9957	chr2:64341714-64518231	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	esv13275	chr2:64342247-64515169	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv1012905	chr2:64342469-64508983	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv1013735	chr2:64342469-64512286	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv3693324	chr2:64342469-64513207	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv999608	chr2:64342469-64517459	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	nsv1000390	chr2:64343861-64512286	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	esv2756924	chr2:64349202-64521290	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
18	nsv1004574	chr2:64360195-64478171	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64340400-64370200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:64347400-64368800	Weak transcription	Spleen	Spleen
3	chr2:64355400-64368800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:64356400-64368800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:64357200-64369600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:64359000-64368800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:64359000-64368800	Weak transcription	Right Ventricle	heart
8	chr2:64360600-64368800	Weak transcription	Fetal Stomach	stomach
9	chr2:64361400-64368800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:64361800-64370000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:64362400-64368800	Weak transcription	NH-A	brain
12	chr2:64362600-64370000	Weak transcription	Ovary	ovary
13	chr2:64363200-64368800	Enhancers	Brain Substantia Nigra	brain
14	chr2:64363200-64368800	Enhancers	Colon Smooth Muscle	Colon
15	chr2:64364000-64370000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:64364000-64370400	Weak transcription	Lung	lung
17	chr2:64364600-64369200	Enhancers	Primary B cells from peripheral blood	blood
18	chr2:64365000-64368800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:64365400-64370800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:64365600-64368800	Weak transcription	Hela-S3	cervix
21	chr2:64365600-64370000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:64365600-64370000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:64365600-64370000	Weak transcription	Placenta	Placenta
24	chr2:64365600-64370000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:64365800-64368800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:64365800-64368800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:64365800-64368800	Weak transcription	Small Intestine	intestine
28	chr2:64365800-64370200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr2:64365800-64370400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:64365800-64370400	Weak transcription	Esophagus	oesophagus
31	chr2:64366000-64368800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:64366000-64368800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:64366000-64369000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:64366400-64368800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:64366400-64371800	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr2:64366600-64368800	Enhancers	Rectal Smooth Muscle	rectum
37	chr2:64366600-64368800	Weak transcription	Thymus	Thymus
38	chr2:64366600-64370000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr2:64366800-64368800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr2:64366800-64368800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:64366800-64371200	Active TSS	Right Atrium	heart
42	chr2:64367000-64368800	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr2:64367000-64368800	Enhancers	Adipose Nuclei	Adipose
44	chr2:64367000-64368800	Enhancers	Osteobl	bone
45	chr2:64367000-64370200	Weak transcription	Left Ventricle	heart
46	chr2:64367000-64370600	Weak transcription	Gastric	stomach
47	chr2:64367200-64368800	Weak transcription	Psoas Muscle	Psoas
48	chr2:64367200-64372400	Active TSS	GM12878-XiMat	blood
49	chr2:64367400-64368800	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr2:64367400-64368800	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links