Variant report

Variant	rs421739
Chromosome Location	chr19:41087759-41087760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41084714..41088277-chr19:41106890..41109795,3	K562	blood:

Variant related genes	Relation type
ENSG00000090006	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16974365	0.94[CHB][hapmap];0.90[CHD][hapmap];0.87[ASN][1000 genomes]
rs2290682	0.93[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs410101	0.81[CEU][hapmap]
rs413901	0.81[CEU][hapmap]
rs418007	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4803346	0.83[ASN][1000 genomes]
rs58633563	0.99[ASN][1000 genomes]
rs62107871	0.83[ASN][1000 genomes]
rs62107874	0.90[ASN][1000 genomes]
rs710160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814518	0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs814519	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS 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	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv911715	chr19:41014922-41141434	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv911716	chr19:41023511-41109456	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv911717	chr19:41023511-41141434	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv911719	chr19:41033109-41147087	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911721	chr19:41040334-41124931	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv869561	chr19:41077513-41139834	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs421739	CA11	cis	cerebellum	SCAN
rs421739	GRWD1	cis	parietal	SCAN
rs421739	QPCTL	cis	cerebellum	SCAN
rs421739	KCNN4	cis	cerebellum	SCAN
rs421739	B9D2	cis	parietal	SCAN
rs421739	GEMIN7	cis	parietal	SCAN
rs421739	PGLYRP1	cis	cerebellum	SCAN
rs421739	DMRTC2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41083600-41091200	Weak transcription	Psoas Muscle	Psoas
2	chr19:41083600-41092800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:41083600-41093600	Weak transcription	Fetal Lung	lung
4	chr19:41083600-41095400	Weak transcription	Fetal Kidney	kidney
5	chr19:41083600-41100400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:41083600-41101000	Weak transcription	HSMMtube	muscle
7	chr19:41084000-41087800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr19:41084000-41089800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:41084000-41091600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:41084000-41094000	Weak transcription	HSMM	muscle
11	chr19:41084000-41095400	Strong transcription	Fetal Intestine Small	intestine
12	chr19:41084000-41097600	Strong transcription	Fetal Stomach	stomach
13	chr19:41084200-41089000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:41084200-41091200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr19:41084200-41093800	Weak transcription	NHEK	skin
16	chr19:41084200-41099800	Weak transcription	Fetal Brain Male	brain
17	chr19:41084400-41090800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:41084400-41091600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:41084400-41092000	Weak transcription	HepG2	liver
20	chr19:41084400-41094200	Weak transcription	HMEC	breast
21	chr19:41084400-41100000	Weak transcription	Stomach Mucosa	stomach
22	chr19:41084600-41091000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:41084600-41095200	Strong transcription	Fetal Muscle Leg	muscle
24	chr19:41084600-41097600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:41084600-41100400	Weak transcription	NHDF-Ad	bronchial
26	chr19:41084600-41102600	Weak transcription	Right Atrium	heart
27	chr19:41084800-41089000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:41084800-41096600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr19:41084800-41097200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr19:41084800-41097600	Strong transcription	Thymus	Thymus
31	chr19:41085000-41091000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr19:41085200-41087800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:41085200-41089200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
34	chr19:41085200-41089800	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr19:41085200-41090800	Strong transcription	Placenta	Placenta
36	chr19:41085200-41094000	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr19:41085400-41089600	Strong transcription	Esophagus	oesophagus
38	chr19:41085400-41089800	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr19:41085400-41090600	Strong transcription	Osteobl	bone
40	chr19:41085400-41094800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr19:41085400-41097200	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr19:41085600-41089800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr19:41085600-41091600	Strong transcription	Fetal Thymus	thymus
44	chr19:41085800-41088800	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr19:41085800-41089600	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr19:41085800-41089800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:41085800-41090200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr19:41085800-41090600	Strong transcription	Dnd41	blood
49	chr19:41085800-41090600	Strong transcription	NHLF	lung
50	chr19:41085800-41090800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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