Variant report

Variant	rs3181039
Chromosome Location	chr3:46421838-46421839
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46420928..46423796-chr3:46462092..46464094,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1001007	0.86[ASN][1000 genomes]
rs11266744	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11574433	0.82[AFR][1000 genomes]
rs11575815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799988	0.80[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs1800023	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800874	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2187673	0.86[ASN][1000 genomes]
rs2187674	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2213290	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2254089	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2734225	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2734648	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2856757	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2856764	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2856765	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3087252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3092962	1.00[YRI][hapmap]
rs3204849	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34682274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35060576	0.86[ASN][1000 genomes]
rs3762823	1.00[YRI][hapmap]
rs41515644	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4560336	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683223	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441971	1.00[YRI][hapmap]
rs6441974	0.86[ASN][1000 genomes]
rs66484806	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs743660	1.00[YRI][hapmap]
rs746492	0.80[ASN][1000 genomes]
rs916091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2756988	chr3:46419634-46444794	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2759146	chr3:46419634-46444794	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3181039	C3orf75	cis	parietal	SCAN
rs3181039	DALRD3	cis	cerebellum	SCAN
rs3181039	CCR5	trans	multi-tissue	Pritchard

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46396000-46422000	Weak transcription	Lung	lung
2	chr3:46404400-46422200	Weak transcription	Thymus	Thymus
3	chr3:46404400-46424600	Weak transcription	Spleen	Spleen
4	chr3:46411400-46422000	Weak transcription	Small Intestine	intestine
5	chr3:46414800-46422000	Weak transcription	Esophagus	oesophagus
6	chr3:46417000-46422200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:46417400-46422000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:46417600-46422000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:46417600-46422000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:46417600-46422000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:46417600-46422000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:46417600-46422000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:46418000-46422000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:46418400-46422000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:46418400-46422000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:46420000-46422000	Enhancers	Dnd41	blood
17	chr3:46420000-46422200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr3:46420000-46423000	Enhancers	Primary B cells from peripheral blood	blood
19	chr3:46420200-46422000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:46420200-46422000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:46420200-46422400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:46420400-46422000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr3:46420400-46422000	Weak transcription	Adipose Nuclei	Adipose
24	chr3:46420400-46422000	Weak transcription	Liver	Liver
25	chr3:46420400-46422000	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:46420400-46422000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:46420400-46422000	Weak transcription	HMEC	breast
28	chr3:46420400-46422000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr3:46420400-46425400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:46420400-46427600	Weak transcription	Pancreas	Pancrea
31	chr3:46420600-46422000	Weak transcription	Placenta	Placenta
32	chr3:46420600-46422000	Weak transcription	Psoas Muscle	Psoas
33	chr3:46420600-46422200	Weak transcription	Stomach Mucosa	stomach
34	chr3:46421000-46422400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:46421000-46423000	Enhancers	Primary B cells from cord blood	blood
36	chr3:46421200-46422200	Weak transcription	Hela-S3	cervix
37	chr3:46421400-46422000	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr3:46421400-46422200	Enhancers	GM12878-XiMat	blood
39	chr3:46421400-46422400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr3:46421400-46422800	Enhancers	Primary T cells fromperipheralblood	blood
41	chr3:46421400-46422800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:46421400-46422800	Enhancers	Fetal Thymus	thymus
43	chr3:46421400-46423000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:46421400-46423400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:46421400-46426000	Enhancers	Fetal Lung	lung
46	chr3:46421600-46422000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:46421600-46422000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr3:46421600-46422000	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr3:46421600-46422000	Enhancers	NHEK	skin
50	chr3:46421600-46422200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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