Variant report

Variant	rs9829155
Chromosome Location	chr3:49817450-49817451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49816078..49819977-chr3:49822757..49825335,4	MCF-7	breast:
2	chr3:49811337..49813407-chr3:49816815..49819575,2	MCF-7	breast:
3	chr3:49812806..49814691-chr3:49816470..49819799,3	K562	blood:
4	chr3:49810586..49813373-chr3:49816346..49818932,2	K562	blood:
5	chr3:49816140..49820070-chr3:49823380..49825359,3	K562	blood:
6	chr3:49816042..49818807-chr3:49821641..49823960,2	MCF-7	breast:
7	chr3:49816876..49821411-chr3:49821519..49825209,5	K562	blood:

Variant related genes	Relation type
ENSG00000244730	Chromatin interaction
ENSG00000176095	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10452032	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1078341	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11130211	0.94[CEU][hapmap];0.85[YRI][hapmap]
rs11130217	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11709734	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11720705	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12637313	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs12715437	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13091525	1.00[ASN][1000 genomes]
rs13096480	1.00[YRI][hapmap]
rs13097720	1.00[ASN][1000 genomes]
rs1352889	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs1491983	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap]
rs1491985	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1586827	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17304079	1.00[ASN][1000 genomes]
rs1799844	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996663	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1996664	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2029591	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs2131108	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2329021	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs28535523	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3020779	1.00[CEU][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs34890793	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap]
rs35012435	1.00[ASN][1000 genomes]
rs35129566	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375092	1.00[ASN][1000 genomes]
rs35491931	1.00[ASN][1000 genomes]
rs35849525	1.00[ASN][1000 genomes]
rs4241405	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs4855833	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs4855845	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4855846	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4855882	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4855885	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs55997059	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58339610	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59357103	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59684465	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61557789	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62260663	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260720	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260723	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62260755	1.00[ASN][1000 genomes]
rs62262061	1.00[ASN][1000 genomes]
rs62262106	1.00[ASN][1000 genomes]
rs62262118	1.00[ASN][1000 genomes]
rs62262722	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262730	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446285	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs6774202	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs6787892	1.00[ASN][1000 genomes]
rs6790568	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6804970	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809879	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71326904	1.00[ASN][1000 genomes]
rs7613603	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615318	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs7620848	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7621797	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628207	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7635601	1.00[ASN][1000 genomes]
rs7637711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649428	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824435	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs9830730	1.00[CEU][hapmap]
rs9835157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836756	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849038	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9851651	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870858	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883000	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]

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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv237797	chr3:49811452-49817742	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv237675	chr3:49811454-49817742	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv965165	chr3:49811992-49817515	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs9829155	ZNF589	cis	parietal	SCAN
rs9829155	QRICH1	cis	cerebellum	SCAN
rs9829155	RNF123	cis	parietal	SCAN
rs9829155	RNF123	cis	Artery Tibial	GTEx
rs9829155	AMT	cis	parietal	SCAN
rs9829155	OR9G4	trans	parietal	SCAN
rs9829155	GMPPB	cis	parietal	SCAN
rs9829155	P4HTM	cis	parietal	SCAN
rs9829155	AMT	cis	lymphoblastoid	seeQTL
rs9829155	GNL3	cis	cerebellum	SCAN
rs9829155	DALRD3	cis	cerebellum	SCAN
rs9829155	DALRD3	cis	parietal	SCAN
rs9829155	AMT	cis	lung	GTEx
rs9829155	AMT	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49775800-49823000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:49776400-49818000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:49776400-49818000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:49776400-49818200	Weak transcription	Fetal Kidney	kidney
5	chr3:49785600-49822400	Weak transcription	HSMMtube	muscle
6	chr3:49785600-49822600	Weak transcription	Esophagus	oesophagus
7	chr3:49785800-49818000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:49786000-49823000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:49786200-49822400	Weak transcription	HMEC	breast
10	chr3:49786400-49817800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:49786600-49817800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:49793800-49817600	Weak transcription	Spleen	Spleen
13	chr3:49795000-49818000	Weak transcription	Psoas Muscle	Psoas
14	chr3:49795000-49819000	Weak transcription	Right Ventricle	heart
15	chr3:49795000-49821000	Weak transcription	K562	blood
16	chr3:49795400-49822400	Weak transcription	Stomach Mucosa	stomach
17	chr3:49802400-49818000	Weak transcription	Right Atrium	heart
18	chr3:49804000-49822600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:49806200-49818800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:49806600-49819000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:49807600-49817800	Weak transcription	Small Intestine	intestine
22	chr3:49807800-49817800	Weak transcription	NH-A	brain
23	chr3:49807800-49822600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:49808200-49818000	Weak transcription	Aorta	Aorta
25	chr3:49808400-49818000	Weak transcription	NHLF	lung
26	chr3:49809200-49817800	Strong transcription	Fetal Thymus	thymus
27	chr3:49809200-49818000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:49809400-49817800	Weak transcription	GM12878-XiMat	blood
29	chr3:49809400-49822800	Weak transcription	A549	lung
30	chr3:49809600-49822400	Weak transcription	NHDF-Ad	bronchial
31	chr3:49810400-49822400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:49812000-49822800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:49812200-49822800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:49812400-49817800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr3:49812400-49818000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:49812600-49817800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:49812600-49817800	Strong transcription	Fetal Intestine Small	intestine
38	chr3:49812600-49819000	Strong transcription	Fetal Stomach	stomach
39	chr3:49812800-49821800	Weak transcription	Fetal Heart	heart
40	chr3:49812800-49822400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:49812800-49822400	Weak transcription	HSMM	muscle
42	chr3:49813000-49817800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:49813000-49819200	Strong transcription	Primary B cells from cord blood	blood
44	chr3:49813200-49817600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:49813200-49817800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:49813200-49817800	Weak transcription	Brain Substantia Nigra	brain
47	chr3:49813200-49817800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:49813200-49817800	Weak transcription	Fetal Muscle Leg	muscle
49	chr3:49813200-49817800	Weak transcription	Gastric	stomach
50	chr3:49813200-49817800	Weak transcription	Left Ventricle	heart

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