Variant report

Variant	rs406683
Chromosome Location	chr3:42545077-42545078
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42200703..42202768-chr3:42543945..42545454,2	MCF-7	breast:
2	chr3:42529189..42533440-chr3:42542111..42547805,7	MCF-7	breast:
3	chr3:42542597..42545270-chr3:42568668..42571142,2	K562	blood:
4	chr3:42518552..42520973-chr3:42544499..42546784,2	MCF-7	breast:
5	chr3:42543941..42547920-chr3:42554474..42558044,4	K562	blood:

Variant related genes	Relation type
ENSG00000182606	Chromatin interaction
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1078008	0.89[CEU][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs182921	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs342542	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs399582	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs421558	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62248806	0.86[AMR][1000 genomes]
rs673560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv527430	chr3:42534042-42557199	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3435194	chr3:42543398-42545496	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs406683	HHATL	cis	cerebellum	SCAN
rs406683	TTC21A	cis	parietal	SCAN
rs406683	CLEC3B	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42542200-42545200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr3:42542600-42545200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr3:42542600-42545200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:42543200-42545200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:42543200-42546200	Active TSS	Rectal Smooth Muscle	rectum
6	chr3:42543800-42545200	Active TSS	Brain Anterior Caudate	brain
7	chr3:42543800-42545600	Active TSS	Brain Angular Gyrus	brain
8	chr3:42543800-42545800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:42544000-42545200	Active TSS	Fetal Intestine Small	intestine
10	chr3:42544000-42545400	Active TSS	Brain Cingulate Gyrus	brain
11	chr3:42544000-42545800	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr3:42544000-42546600	Enhancers	Spleen	Spleen
13	chr3:42544400-42545200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr3:42544400-42545400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr3:42544400-42545400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr3:42544400-42545600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr3:42544400-42546000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr3:42544600-42545200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:42544600-42545200	Flanking Active TSS	Lung	lung
20	chr3:42544600-42545400	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr3:42544600-42545400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr3:42544600-42545600	Enhancers	Primary B cells from cord blood	blood
23	chr3:42544600-42545600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:42544600-42545600	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr3:42544600-42546200	Enhancers	Placenta	Placenta
26	chr3:42544600-42546200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr3:42544600-42548800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:42544600-42551600	Weak transcription	Pancreas	Pancrea
29	chr3:42544800-42545200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:42544800-42545200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr3:42544800-42545200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr3:42544800-42545200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:42544800-42545200	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr3:42544800-42545200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr3:42544800-42545400	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr3:42544800-42545400	Flanking Active TSS	Stomach Mucosa	stomach
37	chr3:42544800-42545400	Weak transcription	K562	blood
38	chr3:42544800-42545600	Enhancers	Gastric	stomach
39	chr3:42544800-42545800	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr3:42544800-42546000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:42544800-42548400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:42544800-42548600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:42544800-42548600	Weak transcription	Esophagus	oesophagus
44	chr3:42544800-42548800	Weak transcription	Left Ventricle	heart
45	chr3:42544800-42548800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr3:42544800-42550600	Weak transcription	Right Atrium	heart
47	chr3:42545000-42545200	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr3:42545000-42545200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:42545000-42545200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
50	chr3:42545000-42545200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links