Variant report

Variant	rs2755097
Chromosome Location	chr1:226167320-226167321
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226164266..226167338-chr1:226248609..226251593,3	MCF-7	breast:
2	chr1:226163855..226167681-chr1:226167885..226170495,3	K562	blood:
3	chr1:226166138..226168581-chr1:226249568..226252466,2	K562	blood:
4	chr1:226028800..226031173-chr1:226165446..226167469,2	MCF-7	breast:
5	chr1:226165055..226167554-chr1:226173060..226175122,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272562	Chromatin interaction
ENSG00000163041	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10915935	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11579912	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586667	0.84[MEX][hapmap]
rs11590226	0.84[MEX][hapmap]
rs11808474	0.84[MEX][hapmap]
rs16845468	0.92[MEX][hapmap]
rs1885254	1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1998273	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]
rs2755092	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2755094	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs2755100	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2816323	0.92[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2816324	0.92[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2816326	0.92[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2816328	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67523369	0.89[EUR][1000 genomes]
rs72757041	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73100512	0.89[EUR][1000 genomes]
rs74148404	1.00[ASN][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
rs2755097	CNIH4	cis	parietal	SCAN

Chromatin state (count:124 , 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	chr1:226156800-226167600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:226157000-226167400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:226162400-226173000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:226163600-226175800	Weak transcription	Aorta	Aorta
6	chr1:226163800-226167400	Weak transcription	Brain Anterior Caudate	brain
7	chr1:226163800-226167400	Weak transcription	Dnd41	blood
8	chr1:226163800-226167400	Weak transcription	HUVEC	blood vessel
9	chr1:226163800-226167600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:226163800-226167600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:226163800-226167600	Weak transcription	NH-A	brain
12	chr1:226163800-226167800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:226163800-226167800	Weak transcription	NHDF-Ad	bronchial
14	chr1:226163800-226168200	Weak transcription	Psoas Muscle	Psoas
15	chr1:226163800-226169000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr1:226163800-226169000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:226163800-226169000	Weak transcription	HMEC	breast
18	chr1:226163800-226174400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:226163800-226175400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:226163800-226175600	Weak transcription	Gastric	stomach
21	chr1:226163800-226175800	Weak transcription	Esophagus	oesophagus
22	chr1:226163800-226178800	Weak transcription	Right Ventricle	heart
23	chr1:226164000-226167400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:226164000-226167400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:226164000-226167400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:226164000-226167400	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:226164000-226167400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:226164000-226167600	Weak transcription	Stomach Mucosa	stomach
29	chr1:226164000-226169000	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:226164000-226171200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:226164000-226171200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:226164000-226172800	Weak transcription	Brain Substantia Nigra	brain
33	chr1:226164200-226167400	Weak transcription	Fetal Brain Female	brain
34	chr1:226164200-226171200	Weak transcription	Brain Angular Gyrus	brain
35	chr1:226164400-226169000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:226164400-226179000	Weak transcription	Small Intestine	intestine
37	chr1:226164600-226167400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:226164600-226169000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:226164600-226169000	Strong transcription	Fetal Stomach	stomach
40	chr1:226164600-226169800	Strong transcription	Thymus	Thymus
41	chr1:226164600-226182800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:226164600-226183000	Strong transcription	Placenta	Placenta
43	chr1:226164800-226167400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:226164800-226167400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:226164800-226169000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:226165000-226167400	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:226165000-226169000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:226165000-226169000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:226165000-226169000	Strong transcription	Fetal Intestine Small	intestine
50	chr1:226165000-226169000	Strong transcription	Fetal Muscle Trunk	muscle

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