Variant report

Variant	rs11575821
Chromosome Location	chr3:46422355-46422356
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	chr3:46414355..46417313-chr3:46422093..46423831,2	K562	blood:
2	chr3:46420928..46423796-chr3:46462092..46464094,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1140865	0.96[EUR][1000 genomes]
rs11574428	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11574429	0.96[EUR][1000 genomes]
rs11574434	0.96[EUR][1000 genomes]
rs11574435	0.81[EUR][1000 genomes]
rs2157061	0.96[EUR][1000 genomes]
rs2157062	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[EUR][1000 genomes]
rs2856758	0.97[EUR][1000 genomes]
rs3092960	0.87[EUR][1000 genomes]
rs3136535	0.92[EUR][1000 genomes]
rs34291293	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34445878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34971514	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35388950	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41490645	0.92[EUR][1000 genomes]
rs4452362	0.81[EUR][1000 genomes]
rs57093591	0.87[EUR][1000 genomes]
rs6441977	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs6762266	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs6770674	0.96[EUR][1000 genomes]
rs6782522	0.96[EUR][1000 genomes]
rs6787972	0.98[EUR][1000 genomes]
rs6791599	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs6791789	0.95[EUR][1000 genomes]
rs6798291	0.96[EUR][1000 genomes]
rs6808835	0.96[EUR][1000 genomes]
rs762790	0.88[EUR][1000 genomes]
rs7652037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs916093	1.00[CEU][hapmap]
rs916094	0.95[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11575821	SCGB3A1	trans	lymphoblastoid	seeQTL
rs11575821	CCR5	trans	multi-tissue	Pritchard

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46404400-46424600	Weak transcription	Spleen	Spleen
2	chr3:46420000-46423000	Enhancers	Primary B cells from peripheral blood	blood
3	chr3:46420200-46422400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:46420400-46425400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:46420400-46427600	Weak transcription	Pancreas	Pancrea
6	chr3:46421000-46422400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:46421000-46423000	Enhancers	Primary B cells from cord blood	blood
8	chr3:46421400-46422400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr3:46421400-46422800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr3:46421400-46422800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:46421400-46422800	Enhancers	Fetal Thymus	thymus
12	chr3:46421400-46423000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:46421400-46423400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:46421400-46426000	Enhancers	Fetal Lung	lung
15	chr3:46421600-46422400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:46421600-46422400	Enhancers	H9 Cell Line	embryonic stem cell
17	chr3:46421600-46422400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr3:46421600-46422600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr3:46421600-46423000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr3:46421600-46423000	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr3:46421600-46423000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:46421600-46423000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr3:46421600-46423000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr3:46421600-46423000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:46421600-46423000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:46421600-46423000	Enhancers	Brain Anterior Caudate	brain
27	chr3:46421600-46424000	Enhancers	Fetal Brain Male	brain
28	chr3:46421800-46422600	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr3:46421800-46423000	Enhancers	Primary T cells from cord blood	blood
30	chr3:46421800-46423000	Enhancers	Primary hematopoietic stem cells	blood
31	chr3:46421800-46425000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:46422000-46422400	Enhancers	H1 Cell Line	embryonic stem cell
33	chr3:46422000-46422400	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr3:46422000-46422400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:46422000-46422400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:46422000-46422400	Enhancers	Esophagus	oesophagus
37	chr3:46422000-46422400	Bivalent Enhancer	Fetal Muscle Leg	muscle
38	chr3:46422000-46422400	Enhancers	Gastric	stomach
39	chr3:46422000-46422400	Enhancers	Lung	lung
40	chr3:46422000-46422400	Enhancers	Psoas Muscle	Psoas
41	chr3:46422000-46422400	Flanking Active TSS	Dnd41	blood
42	chr3:46422000-46422400	Flanking Active TSS	NHEK	skin
43	chr3:46422000-46422400	Bivalent Enhancer	Osteobl	bone
44	chr3:46422000-46422600	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr3:46422000-46422600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:46422000-46422600	Enhancers	Placenta	Placenta
47	chr3:46422000-46422600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr3:46422000-46422800	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr3:46422000-46422800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:46422000-46422800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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