Variant report

Variant	rs2816323
Chromosome Location	chr1:226183594-226183595
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226076245..226078992-chr1:226182776..226185371,2	K562	blood:
2	chr1:226183087..226192322-chr1:226243551..226254243,95	K562	blood:
3	chr1:226069274..226070953-chr1:226180854..226183828,2	K562	blood:
4	chr1:226182615..226184840-chr1:226309773..226312606,2	K562	blood:
5	chr1:226183457..226185204-chr1:226185792..226188417,2	MCF-7	breast:
6	chr1:226183543..226186620-chr1:226307621..226310458,4	MCF-7	breast:
7	chr1:226116139..226117660-chr1:226183554..226185717,2	K562	blood:
8	chr1:226183330..226185192-chr1:226257452..226258976,2	K562	blood:
9	chr1:226183029..226192481-chr1:226247725..226253108,31	MCF-7	breast:
10	chr1:226178791..226193771-chr1:226246813..226256535,111	K562	blood:
11	chr1:226128249..226131206-chr1:226183355..226186059,2	K562	blood:
12	chr1:225632657..225635050-chr1:226182326..226184522,2	MCF-7	breast:
13	chr1:226175987..226179180-chr1:226182240..226184777,3	MCF-7	breast:
14	chr1:226108702..226117785-chr1:226183554..226190529,14	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196187	Chromatin interaction
ENSG00000243709	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000272562	Chromatin interaction
ENSG00000143768	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000143811	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11586667	0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs11590226	0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs11808474	0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs11809941	0.86[EUR][1000 genomes]
rs12735124	0.82[JPT][hapmap]
rs16845468	0.84[MEX][hapmap];0.86[EUR][1000 genomes]
rs16845499	0.82[JPT][hapmap]
rs16845535	0.82[JPT][hapmap]
rs1885254	0.84[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs1998273	0.88[CEU][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2755092	0.84[EUR][1000 genomes]
rs2755094	1.00[CEU][hapmap];0.82[TSI][hapmap]
rs2755095	0.88[GIH][hapmap]
rs2755097	0.92[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2816324	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816326	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2816328	0.81[EUR][1000 genomes]
rs3748813	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs66514719	0.86[EUR][1000 genomes]
rs66791434	0.86[EUR][1000 genomes]
rs66934363	0.86[EUR][1000 genomes]
rs67269884	0.86[EUR][1000 genomes]
rs67523369	0.81[EUR][1000 genomes]
rs73100512	0.81[EUR][1000 genomes]
rs73100535	0.86[EUR][1000 genomes]
rs7554619	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2816323	CNIH4	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226129600-226185600	Weak transcription	Right Atrium	heart
2	chr1:226165000-226183600	Strong transcription	Adipose Nuclei	Adipose
3	chr1:226165000-226186000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:226165400-226183800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:226165600-226184400	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:226167000-226185000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:226167400-226183600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:226169200-226183600	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:226169800-226183600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:226169800-226183600	Weak transcription	Stomach Mucosa	stomach
11	chr1:226170000-226183600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:226170000-226183800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:226170000-226185800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:226170200-226184400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:226170200-226186200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:226170400-226184000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:226170600-226183600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:226171000-226183800	Strong transcription	Primary B cells from peripheral blood	blood
19	chr1:226171400-226184600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:226171600-226183600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:226171600-226184000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:226171600-226185800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:226173000-226183800	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr1:226176000-226183600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr1:226177200-226183800	Strong transcription	Fetal Intestine Large	intestine
26	chr1:226177200-226184200	Strong transcription	HSMM	muscle
27	chr1:226178000-226183600	Strong transcription	HMEC	breast
28	chr1:226180200-226185600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:226180200-226186200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:226180400-226185600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:226180400-226186000	Weak transcription	Ovary	ovary
32	chr1:226180600-226183600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:226180600-226183800	Weak transcription	Fetal Heart	heart
34	chr1:226180600-226185400	Weak transcription	Fetal Brain Male	brain
35	chr1:226180600-226185800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:226180800-226183600	Weak transcription	Small Intestine	intestine
37	chr1:226180800-226185000	Weak transcription	Brain Substantia Nigra	brain
38	chr1:226180800-226185200	Weak transcription	Fetal Kidney	kidney
39	chr1:226180800-226185600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:226180800-226185600	Weak transcription	Brain Germinal Matrix	brain
41	chr1:226180800-226185600	Weak transcription	Right Ventricle	heart
42	chr1:226180800-226186400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:226181600-226183600	Weak transcription	Fetal Brain Female	brain
44	chr1:226181600-226184400	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr1:226181600-226184600	Genic enhancers	HepG2	liver
46	chr1:226181600-226185200	Weak transcription	Esophagus	oesophagus
47	chr1:226181800-226183800	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:226181800-226186000	Weak transcription	Aorta	Aorta
49	chr1:226181800-226186200	Weak transcription	Gastric	stomach
50	chr1:226182000-226183600	Weak transcription	Brain Anterior Caudate	brain

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