Variant report

Variant	rs3099968
Chromosome Location	chr2:39033590-39033591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38976392..38979029-chr2:39027754..39033871,6	K562	blood:
2	chr2:39013355..39015895-chr2:39031959..39033767,2	K562	blood:
3	chr2:39032198..39035187-chr2:39047405..39049183,2	MCF-7	breast:
4	chr2:38976572..38979888-chr2:39032371..39035700,3	K562	blood:
5	chr2:38976891..38979056-chr2:39028521..39033921,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1010859	0.83[ASW][hapmap];0.88[JPT][hapmap]
rs10197412	0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap]
rs10865143	0.90[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11124646	0.88[CEU][hapmap]
rs11898812	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs12468732	0.85[EUR][1000 genomes]
rs12474770	0.81[ASN][1000 genomes]
rs12618118	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs12621103	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.85[ASN][1000 genomes]
rs13024811	0.81[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs1529625	0.82[CHB][hapmap]
rs1979143	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2037875	0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap]
rs3097713	0.95[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[ASN][1000 genomes]
rs3097714	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs3099961	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3099965	0.95[ASN][1000 genomes]
rs3099971	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099975	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099977	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099980	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099990	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099992	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3100000	1.00[JPT][hapmap]
rs3108666	0.82[ASN][1000 genomes]
rs3112142	0.83[CEU][hapmap];0.90[CHB][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3112143	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3112150	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3112152	0.82[ASN][1000 genomes]
rs3112156	0.82[ASN][1000 genomes]
rs3112159	0.83[ASW][hapmap];0.88[JPT][hapmap]
rs3112161	0.82[ASN][1000 genomes]
rs3112163	0.83[ASW][hapmap];1.00[JPT][hapmap]
rs3112178	0.95[CEU][hapmap];0.88[JPT][hapmap]
rs3112183	0.80[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.82[ASN][1000 genomes]
rs3112184	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112186	0.92[ASN][1000 genomes]
rs3112188	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112189	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112191	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112192	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112194	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3112196	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3112198	0.91[ASN][1000 genomes]
rs3112204	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112209	0.87[AMR][1000 genomes]
rs3112215	0.84[CEU][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3134628	0.88[CHD][hapmap];0.81[GIH][hapmap];0.82[ASN][1000 genomes]
rs3134629	0.82[ASN][1000 genomes]
rs3134630	0.82[ASN][1000 genomes]
rs3134637	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs35387882	0.87[ASN][1000 genomes]
rs3731838	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs4670268	0.86[JPT][hapmap]
rs4670892	0.81[ASN][1000 genomes]
rs6544175	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6715866	0.82[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.81[ASN][1000 genomes]
rs6717670	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6746818	0.82[CHB][hapmap]
rs756338	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3099968	DHX57	cis	cerebellum	SCAN
rs3099968	MORN2	cis	parietal	SCAN
rs3099968	ITGB1	trans	parietal	SCAN
rs3099968	GALM	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39005800-39037400	Weak transcription	Esophagus	oesophagus
2	chr2:39006000-39037600	Weak transcription	Aorta	Aorta
3	chr2:39006000-39037600	Weak transcription	Gastric	stomach
4	chr2:39006400-39037800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:39006400-39045600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:39006600-39033600	Weak transcription	GM12878-XiMat	blood
8	chr2:39006600-39038200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:39009000-39037400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:39009200-39037600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:39009200-39037600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr2:39009200-39037600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:39009200-39037600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:39009200-39037600	Weak transcription	NHDF-Ad	bronchial
15	chr2:39009200-39037800	Weak transcription	NHEK	skin
16	chr2:39009200-39042600	Weak transcription	Fetal Kidney	kidney
17	chr2:39009200-39050000	Weak transcription	HMEC	breast
18	chr2:39009200-39052800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:39009400-39037600	Weak transcription	NHLF	lung
20	chr2:39009600-39037600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:39009600-39037600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:39012000-39037600	Weak transcription	Pancreas	Pancrea
23	chr2:39012200-39037600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:39017600-39042200	Weak transcription	Small Intestine	intestine
25	chr2:39018400-39037600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:39019000-39057800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr2:39021400-39038000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:39021600-39038000	Weak transcription	Colonic Mucosa	Colon
29	chr2:39022000-39042600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:39022000-39066800	Weak transcription	Stomach Mucosa	stomach
31	chr2:39022400-39037400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr2:39024000-39053000	Weak transcription	Psoas Muscle	Psoas
33	chr2:39024400-39034400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:39025400-39038000	Weak transcription	HUVEC	blood vessel
35	chr2:39025600-39037600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:39025600-39042400	Weak transcription	Hela-S3	cervix
37	chr2:39025600-39042400	Weak transcription	HSMM	muscle
38	chr2:39025800-39037400	Weak transcription	Liver	Liver
39	chr2:39025800-39037800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:39026000-39037600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:39026600-39079800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr2:39027200-39034200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:39027400-39034000	Strong transcription	Brain Germinal Matrix	brain
44	chr2:39027400-39034600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:39027600-39033800	Strong transcription	Fetal Brain Female	brain
46	chr2:39027600-39034200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:39028800-39034200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:39029000-39033600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:39029200-39034000	Strong transcription	Fetal Muscle Leg	muscle
50	chr2:39029600-39033600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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