Variant report

Variant	rs6427286
Chromosome Location	chr1:155723297-155723298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155722602..155725038-chr1:155735095..155737903,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10908470	0.91[JPT][hapmap]
rs10908471	0.92[JPT][hapmap]
rs10908479	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10908480	0.83[ASN][1000 genomes]
rs10908481	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10908482	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11264409	0.97[ASN][1000 genomes]
rs11264410	0.91[ASN][1000 genomes]
rs12035524	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12040894	0.87[ASN][1000 genomes]
rs12047756	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12081192	0.85[ASN][1000 genomes]
rs12407800	0.82[ASN][1000 genomes]
rs12744132	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1556488	0.81[JPT][hapmap]
rs2048431	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2175391	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2297775	0.93[ASN][1000 genomes]
rs2666826	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs28582361	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28662267	0.90[ASN][1000 genomes]
rs2948071	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2948072	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2985707	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs348196	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3738590	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3820594	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs3892792	0.92[JPT][hapmap]
rs4278368	0.97[ASN][1000 genomes]
rs475550	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs490608	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6427287	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs644853	0.84[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes]
rs6662953	0.86[ASN][1000 genomes]
rs6665227	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs670876	0.91[CHB][hapmap]
rs678157	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs708611	0.95[CHB][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7521594	0.80[ASN][1000 genomes]
rs7541060	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7550402	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs821551	0.85[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs822025	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs822478	0.85[CHB][hapmap]
rs822490	0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs822527	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs860295	0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9426933	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	esv3436971	chr1:155618172-155733386	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv3338099	chr1:155618190-155733359	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv3065	chr1:155682768-155727524	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6427286	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155715400-155725600	Weak transcription	Fetal Brain Male	brain
2	chr1:155715400-155726200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:155715400-155730000	Weak transcription	Stomach Mucosa	stomach
4	chr1:155715400-155739200	Weak transcription	Fetal Heart	heart
5	chr1:155715400-155789200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:155715600-155725000	Weak transcription	Small Intestine	intestine
7	chr1:155715600-155725200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:155715600-155725200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:155715600-155725400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:155715600-155726800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:155715600-155764600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:155716000-155725000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:155716000-155793400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:155716200-155726800	Weak transcription	A549	lung
15	chr1:155716600-155725400	Strong transcription	Fetal Intestine Small	intestine
16	chr1:155716600-155781800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:155717200-155725000	Strong transcription	Lung	lung
18	chr1:155717200-155725600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:155717200-155761000	Strong transcription	Fetal Stomach	stomach
20	chr1:155717400-155731000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:155717400-155733400	Strong transcription	Brain Anterior Caudate	brain
22	chr1:155717400-155795800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:155717600-155733800	Strong transcription	Spleen	Spleen
24	chr1:155717600-155750200	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:155718000-155729400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:155718200-155729400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:155718800-155726800	Weak transcription	Psoas Muscle	Psoas
28	chr1:155719200-155723400	Weak transcription	NHDF-Ad	bronchial
29	chr1:155720000-155732000	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr1:155720200-155732800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr1:155720200-155732800	Strong transcription	Osteobl	bone
32	chr1:155720200-155733000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr1:155720200-155733800	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:155720200-155745400	Strong transcription	Fetal Muscle Leg	muscle
35	chr1:155720200-155748600	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:155720200-155748800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr1:155720200-155748800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:155720200-155749000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:155720200-155749600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:155720200-155750200	Strong transcription	Primary T cells from cord blood	blood
41	chr1:155720200-155750600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:155720200-155755800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:155720200-155756200	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:155720200-155756600	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:155720200-155798200	Strong transcription	Fetal Thymus	thymus
46	chr1:155720200-155803600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:155720400-155723800	Strong transcription	Brain Hippocampus Middle	brain
48	chr1:155720400-155724000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:155720400-155724200	Strong transcription	K562	blood
50	chr1:155720400-155725400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links