Variant report

Variant	rs7516231
Chromosome Location	chr1:161026079-161026080
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161014603..161017982-chr1:161025944..161029502,5	K562	blood:
2	chr1:161018354..161021283-chr1:161024769..161026655,3	K562	blood:
3	chr1:161024286..161026586-chr1:161059116..161061202,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158773	Chromatin interaction
ENSG00000143217	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12036299	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1556259	1.00[CEU][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs1556260	1.00[CEU][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs16832617	0.94[ASW][hapmap];0.87[CEU][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap]
rs1974140	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2073653	1.00[CEU][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs3766382	0.81[EUR][1000 genomes]
rs3766383	0.81[EUR][1000 genomes]
rs4617422	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs58318788	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58974723	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6427573	1.00[CEU][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs6660240	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6686076	1.00[CEU][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs6695707	0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7516231	ITLN1	cis	cerebellum	SCAN
rs7516231	SDHC	cis	parietal	SCAN
rs7516231	FCGR2A	cis	parietal	SCAN
rs7516231	FCRL3	cis	cerebellum	SCAN
rs7516231	ASH1L	cis	cerebellum	SCAN
rs7516231	F11R	cis	cerebellum	SCAN
rs7516231	ARHGEF11	cis	cerebellum	SCAN
rs7516231	ABCA2	trans	cerebellum	SCAN
rs7516231	KIRREL	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161016400-161037800	Weak transcription	Colonic Mucosa	Colon
2	chr1:161016600-161028000	Weak transcription	Brain Substantia Nigra	brain
3	chr1:161016800-161029200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:161017000-161029400	Strong transcription	Primary T cells from cord blood	blood
5	chr1:161017000-161031600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:161017000-161032200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:161017200-161029200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:161017200-161030000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:161017400-161027400	Strong transcription	Primary hematopoietic stem cells	blood
10	chr1:161017400-161027400	Strong transcription	Dnd41	blood
11	chr1:161017400-161030000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:161017400-161031000	Strong transcription	Thymus	Thymus
13	chr1:161017600-161034400	Strong transcription	Fetal Thymus	thymus
14	chr1:161017800-161026200	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:161018000-161027400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:161018200-161026800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:161018400-161026400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:161018400-161027400	Strong transcription	GM12878-XiMat	blood
19	chr1:161018600-161032400	Strong transcription	Primary B cells from cord blood	blood
20	chr1:161018600-161033600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:161018800-161028200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:161019000-161026600	Strong transcription	Placenta	Placenta
23	chr1:161019400-161029400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr1:161020800-161027400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr1:161021400-161034000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr1:161021600-161029400	Weak transcription	Stomach Mucosa	stomach
27	chr1:161021600-161033000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:161021600-161038400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:161022600-161028200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:161022800-161029200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:161022800-161031800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:161023200-161029800	Weak transcription	Gastric	stomach
33	chr1:161024400-161030600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:161024800-161026200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:161024800-161038200	Weak transcription	Lung	lung
36	chr1:161025000-161027200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:161025200-161026200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:161025200-161026200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:161025400-161026200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:161025800-161026400	Strong transcription	Liver	Liver
41	chr1:161025800-161026800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:161025800-161028000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr1:161026000-161026200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:161026000-161026400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:161026000-161026400	Genic enhancers	Spleen	Spleen
46	chr1:161026000-161027000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr1:161026000-161027400	Strong transcription	Esophagus	oesophagus

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