Variant report

Variant	rs1998273
Chromosome Location	chr1:226184438-226184439
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 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	chr1:226182615..226184840-chr1:226309773..226312606,2	K562	blood:
4	chr1:226183457..226185204-chr1:226185792..226188417,2	MCF-7	breast:
5	chr1:226183543..226186620-chr1:226307621..226310458,4	MCF-7	breast:
6	chr1:226116139..226117660-chr1:226183554..226185717,2	K562	blood:
7	chr1:226183330..226185192-chr1:226257452..226258976,2	K562	blood:
8	chr1:226177708..226179904-chr1:226184290..226186847,2	MCF-7	breast:
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:
15	chr1:225724327..225726333-chr1:226183688..226185527,2	MCF-7	breast:

No data

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

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

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

rs_ID	r²[population]
rs10915935	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11579912	0.85[ASN][1000 genomes]
rs11586667	0.91[MEX][hapmap];0.82[EUR][1000 genomes]
rs11590226	0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs11808474	0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs11809941	0.83[EUR][1000 genomes]
rs16845468	0.83[MEX][hapmap];0.83[EUR][1000 genomes]
rs1885254	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2755092	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2755094	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs2755097	0.85[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2755100	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2816323	0.88[CEU][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2816324	0.87[CEU][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2816326	0.88[CEU][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2816328	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66514719	0.83[EUR][1000 genomes]
rs66791434	0.83[EUR][1000 genomes]
rs66934363	0.83[EUR][1000 genomes]
rs67269884	0.83[EUR][1000 genomes]
rs67523369	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72757041	0.87[EUR][1000 genomes]
rs73100512	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73100535	0.83[EUR][1000 genomes]
rs74148404	0.85[ASN][1000 genomes]
rs7554619	0.83[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
rs1998273	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	chr1:226165000-226186000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:226167000-226185000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:226170000-226185800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:226170200-226186200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:226171400-226184600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:226171600-226185800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:226180200-226185600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:226180200-226186200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:226180400-226185600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:226180400-226186000	Weak transcription	Ovary	ovary
12	chr1:226180600-226185400	Weak transcription	Fetal Brain Male	brain
13	chr1:226180600-226185800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:226180800-226185000	Weak transcription	Brain Substantia Nigra	brain
15	chr1:226180800-226185200	Weak transcription	Fetal Kidney	kidney
16	chr1:226180800-226185600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:226180800-226185600	Weak transcription	Brain Germinal Matrix	brain
18	chr1:226180800-226185600	Weak transcription	Right Ventricle	heart
19	chr1:226180800-226186400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:226181600-226184600	Genic enhancers	HepG2	liver
21	chr1:226181600-226185200	Weak transcription	Esophagus	oesophagus
22	chr1:226181800-226186000	Weak transcription	Aorta	Aorta
23	chr1:226181800-226186200	Weak transcription	Gastric	stomach
24	chr1:226182200-226185600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:226182600-226185200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr1:226182600-226185200	Weak transcription	Spleen	Spleen
27	chr1:226182800-226185200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:226182800-226185200	Weak transcription	Fetal Stomach	stomach
29	chr1:226182800-226185200	Weak transcription	Lung	lung
30	chr1:226182800-226185600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:226182800-226185800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:226182800-226186200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:226183000-226184800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr1:226183000-226184800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:226183000-226184800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:226183000-226185200	Weak transcription	Placenta	Placenta
37	chr1:226183000-226185400	Weak transcription	Brain Angular Gyrus	brain
38	chr1:226183000-226185600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:226183000-226185600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr1:226183000-226185600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:226183000-226185800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:226183000-226185800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr1:226183000-226186000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:226183000-226186200	Weak transcription	Left Ventricle	heart
45	chr1:226183200-226185000	Transcr. at gene 5' and 3'	K562	blood
46	chr1:226183200-226185200	Genic enhancers	Primary T cells from cord blood	blood
47	chr1:226183200-226185200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:226183200-226185400	Enhancers	Liver	Liver
49	chr1:226183200-226185600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:226183200-226185600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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