Variant report

Variant	rs6791542
Chromosome Location	chr3:48787219-48787220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48781538..48784352-chr3:48787212..48789298,3	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 40 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10780033	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs10865952	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11130176	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1134591	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.80[EUR][1000 genomes]
rs11705888	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706983	1.00[CHD][hapmap]
rs11708786	1.00[CHD][hapmap]
rs11713694	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11715689	0.95[ASN][1000 genomes]
rs11715713	0.90[ASN][1000 genomes]
rs11715835	0.90[ASN][1000 genomes]
rs11719291	1.00[CHD][hapmap]
rs11920534	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs11924597	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11928552	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs12493289	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12493578	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs12497850	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13084000	0.90[ASN][1000 genomes]
rs13087930	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13092715	0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs13315711	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs13434258	1.00[CHD][hapmap]
rs1352420	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28642807	0.83[EUR][1000 genomes]
rs34037363	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs35064573	1.00[CHD][hapmap]
rs3774628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4858798	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4858828	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4858831	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs4974079	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs4974082	0.80[EUR][1000 genomes]
rs4974085	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs4974087	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs6442130	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6446196	0.80[EUR][1000 genomes]
rs6446252	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6446253	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6788650	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7373778	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7430501	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs7431710	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs7431857	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs7616815	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7623023	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7627404	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7628719	0.80[EUR][1000 genomes]
rs7630742	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7636057	0.80[EUR][1000 genomes]
rs7639332	0.82[EUR][1000 genomes]
rs7647813	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs7649458	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.81[EUR][1000 genomes]
rs9311430	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9311432	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9311433	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9311434	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9637481	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9681717	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9682444	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9754878	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9755490	1.00[CEU][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9830636	0.80[EUR][1000 genomes]
rs9835307	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9840684	0.84[EUR][1000 genomes]
rs9850134	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs9873726	1.00[CHB][hapmap]
rs9876848	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9879971	0.84[EUR][1000 genomes]
rs9882549	1.00[CHD][hapmap]
rs9884022	1.00[CEU][hapmap];1.00[JPT][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	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv3407876	chr3:48774454-48823998	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:40)

SNP	Gene	Cis/trans	Tissue	Source
rs6791542	NICN1	cis	multi-tissue	Pritchard
rs6791542	NCKIPSD	cis	cerebellum	SCAN
rs6791542	TLR9	cis	parietal	SCAN
rs6791542	WDR6	cis	Esophagus Mucosa	GTEx
rs6791542	WDR6	cis	Whole Blood	GTEx
rs6791542	NCKIPSD	cis	Esophagus Muscularis	GTEx
rs6791542	WDR6	cis	lymphoblastoid	seeQTL
rs6791542	WDR6	cis	Liver	GTEx
rs6791542	P4HTM	cis	cerebellum	SCAN
rs6791542	WDR6	cis	Heart Left Ventricle	GTEx
rs6791542	AMT	cis	parietal	SCAN
rs6791542	CCDC71	cis	cerebellum	SCAN
rs6791542	NICN1-AS1	cis	Thyroid	GTEx
rs6791542	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs6791542	PHF7	cis	parietal	SCAN
rs6791542	WDR6	cis	uninvolved skin	skin_eQTL
rs6791542	WDR6	cis	parietal	SCAN
rs6791542	ARIH2	cis	Thyroid	GTEx
rs6791542	NICN1	cis	Thyroid	GTEx
rs6791542	WDR6	cis	Artery Tibial	GTEx
rs6791542	AMT	cis	Whole Blood	GTEx
rs6791542	P4HTM	cis	parietal	SCAN
rs6791542	DALRD3	cis	parietal	SCAN
rs6791542	DALRD3	cis	cerebellum	SCAN
rs6791542	AMT	cis	cerebellum	SCAN
rs6791542	NCKIPSD	cis	Muscle Skeletal	GTEx
rs6791542	NCKIPSD	cis	Nerve Tibial	GTEx
rs6791542	AMT	cis	multi-tissue	Pritchard
rs6791542	NCKIPSD	cis	multi-tissue	Pritchard
rs6791542	WDR6	cis	lung	GTEx
rs6791542	WDR6	cis	multi-tissue	Pritchard
rs6791542	WDR6	cis	Muscle Skeletal	GTEx
rs6791542	AMT	cis	Thyroid	GTEx
rs6791542	WDR6	cis	Esophagus Muscularis	GTEx
rs6791542	WDR6	cis	Adipose Subcutaneous	GTEx
rs6791542	WDR6	cis	Nerve Tibial	GTEx
rs6791542	NCKIPSD	cis	parietal	SCAN
rs6791542	AMT	cis	Artery Aorta	GTEx
rs6791542	CCDC36	cis	Artery Tibial	GTEx
rs6791542	WDR6	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48777600-48787800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:48777800-48788000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:48777800-48788800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:48777800-48807400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:48778000-48788000	Weak transcription	HUVEC	blood vessel
6	chr3:48778000-48788200	Weak transcription	NH-A	brain
7	chr3:48778000-48788400	Weak transcription	GM12878-XiMat	blood
8	chr3:48778000-48789000	Weak transcription	NHEK	skin
9	chr3:48778000-48807200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:48778200-48787800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:48778200-48788400	Weak transcription	Fetal Brain Male	brain
12	chr3:48778200-48814400	Weak transcription	Fetal Heart	heart
13	chr3:48778200-48820200	Weak transcription	Fetal Kidney	kidney
14	chr3:48778200-48836600	Weak transcription	A549	lung
15	chr3:48778400-48796000	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:48778600-48789000	Weak transcription	Small Intestine	intestine
17	chr3:48778600-48826000	Weak transcription	Stomach Mucosa	stomach
18	chr3:48779000-48788400	Weak transcription	Colonic Mucosa	Colon
19	chr3:48779000-48788400	Weak transcription	Esophagus	oesophagus
20	chr3:48780600-48788400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:48780600-48788600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:48781800-48788000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr3:48782200-48814400	Weak transcription	K562	blood
24	chr3:48783000-48788200	Weak transcription	Fetal Lung	lung
25	chr3:48783200-48788800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:48783200-48790000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:48783400-48811400	Strong transcription	Fetal Stomach	stomach
28	chr3:48783600-48788000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:48784000-48790000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:48784400-48789400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr3:48784400-48794600	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr3:48784600-48790200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:48784800-48789600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:48784800-48790000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr3:48784800-48790200	Strong transcription	Primary T cells from cord blood	blood
36	chr3:48784800-48790200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:48784800-48791400	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:48784800-48791800	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:48784800-48793800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:48785000-48788200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr3:48785000-48788400	Strong transcription	Fetal Intestine Small	intestine
42	chr3:48785000-48790200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:48785000-48790200	Strong transcription	Stomach Smooth Muscle	stomach
44	chr3:48785000-48790400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr3:48785000-48791000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:48785200-48788000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:48785200-48788400	Weak transcription	Brain Germinal Matrix	brain
48	chr3:48785200-48788400	Weak transcription	HMEC	breast
49	chr3:48785200-48789400	Strong transcription	Fetal Intestine Large	intestine
50	chr3:48785200-48789800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links