Variant report

Variant	rs2816324
Chromosome Location	chr1:226183357-226183358
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 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	chr1:226183330..226185192-chr1:226257452..226258976,2	K562	blood:
6	chr1:226183029..226192481-chr1:226247725..226253108,31	MCF-7	breast:
7	chr1:226178791..226193771-chr1:226246813..226256535,111	K562	blood:
8	chr1:226128249..226131206-chr1:226183355..226186059,2	K562	blood:
9	chr1:225632657..225635050-chr1:226182326..226184522,2	MCF-7	breast:
10	chr1:226175987..226179180-chr1:226182240..226184777,3	MCF-7	breast:

No data

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

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

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	0.92[JPT][hapmap]
rs16845468	0.84[MEX][hapmap];0.86[EUR][1000 genomes]
rs1885254	0.84[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs1998273	0.87[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]
rs2816323	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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[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	0.92[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
rs2816324	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	chr1:226165200-226183400	Strong transcription	Osteobl	bone
5	chr1:226165400-226183400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:226165400-226183400	Strong transcription	Stomach Smooth Muscle	stomach
7	chr1:226165400-226183800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:226165600-226184400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:226167000-226185000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:226167400-226183600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:226169200-226183600	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:226169800-226183600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:226169800-226183600	Weak transcription	Stomach Mucosa	stomach
14	chr1:226170000-226183600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:226170000-226183800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:226170000-226185800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:226170200-226184400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:226170200-226186200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:226170400-226184000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:226170600-226183600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:226171000-226183400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:226171000-226183800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr1:226171400-226184600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:226171600-226183600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:226171600-226184000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:226171600-226185800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:226172200-226183400	Strong transcription	A549	lung
28	chr1:226173000-226183800	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr1:226176000-226183600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr1:226177200-226183400	Strong transcription	Primary B cells from cord blood	blood
31	chr1:226177200-226183800	Strong transcription	Fetal Intestine Large	intestine
32	chr1:226177200-226184200	Strong transcription	HSMM	muscle
33	chr1:226178000-226183600	Strong transcription	HMEC	breast
34	chr1:226178800-226183400	Strong transcription	NHDF-Ad	bronchial
35	chr1:226179600-226183400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:226180000-226183400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:226180200-226185600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr1:226180200-226186200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:226180400-226185600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:226180400-226186000	Weak transcription	Ovary	ovary
41	chr1:226180600-226183600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:226180600-226183800	Weak transcription	Fetal Heart	heart
43	chr1:226180600-226185400	Weak transcription	Fetal Brain Male	brain
44	chr1:226180600-226185800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:226180800-226183600	Weak transcription	Small Intestine	intestine
46	chr1:226180800-226185000	Weak transcription	Brain Substantia Nigra	brain
47	chr1:226180800-226185200	Weak transcription	Fetal Kidney	kidney
48	chr1:226180800-226185600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:226180800-226185600	Weak transcription	Brain Germinal Matrix	brain
50	chr1:226180800-226185600	Weak transcription	Right Ventricle	heart

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