Variant report

Variant	rs398162
Chromosome Location	chr19:41092561-41092562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIX5	chr19:41090616-41092588	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41089392..41091268-chr19:41092459..41096170,3	K562	blood:
2	chr19:41083433..41086530-chr19:41091695..41093965,3	MCF-7	breast:
3	chr19:41089494..41092756-chr19:41107049..41110047,4	K562	blood:

Variant related genes	Relation type
SHKBP1	TF binding region
ENSG00000160410	Chromatin interaction
ENSG00000090006	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs268682	1.00[EUR][1000 genomes]
rs366973	1.00[EUR][1000 genomes]
rs400195	1.00[EUR][1000 genomes]
rs403842	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4150980	1.00[EUR][1000 genomes]
rs4150982	1.00[EUR][1000 genomes]
rs8112927	1.00[EUR][1000 genomes]
rs922216	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
14	nsv911724	chr19:41089505-41165252	Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
15	nsv911725	chr19:41090190-41114065	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS 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	25 gene(s)	inside rSNPs	diseases
16	nsv911726	chr19:41090190-41141434	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41083600-41092800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41083600-41093600	Weak transcription	Fetal Lung	lung
3	chr19:41083600-41095400	Weak transcription	Fetal Kidney	kidney
4	chr19:41083600-41100400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:41083600-41101000	Weak transcription	HSMMtube	muscle
6	chr19:41084000-41094000	Weak transcription	HSMM	muscle
7	chr19:41084000-41095400	Strong transcription	Fetal Intestine Small	intestine
8	chr19:41084000-41097600	Strong transcription	Fetal Stomach	stomach
9	chr19:41084200-41093800	Weak transcription	NHEK	skin
10	chr19:41084200-41099800	Weak transcription	Fetal Brain Male	brain
11	chr19:41084400-41094200	Weak transcription	HMEC	breast
12	chr19:41084400-41100000	Weak transcription	Stomach Mucosa	stomach
13	chr19:41084600-41095200	Strong transcription	Fetal Muscle Leg	muscle
14	chr19:41084600-41097600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:41084600-41100400	Weak transcription	NHDF-Ad	bronchial
16	chr19:41084600-41102600	Weak transcription	Right Atrium	heart
17	chr19:41084800-41096600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr19:41084800-41097200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr19:41084800-41097600	Strong transcription	Thymus	Thymus
20	chr19:41085200-41094000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:41085400-41094800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:41085400-41097200	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr19:41085800-41095200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:41085800-41095200	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr19:41086000-41094600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr19:41086000-41094800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:41086000-41095200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr19:41086000-41095200	Strong transcription	Stomach Smooth Muscle	stomach
29	chr19:41086000-41097200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:41086000-41097800	Strong transcription	Primary T cells from cord blood	blood
31	chr19:41086400-41100400	Weak transcription	K562	blood
32	chr19:41086600-41097400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr19:41086800-41097400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:41086800-41097400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:41086800-41099000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr19:41086800-41100000	Weak transcription	Fetal Brain Female	brain
37	chr19:41086800-41100600	Weak transcription	Brain Angular Gyrus	brain
38	chr19:41087000-41092800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr19:41087000-41093400	Strong transcription	Primary hematopoietic stem cells	blood
40	chr19:41087000-41097000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:41087000-41097200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr19:41087200-41096800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:41087200-41100400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr19:41087600-41102600	Weak transcription	Small Intestine	intestine
45	chr19:41087800-41093200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:41087800-41095600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr19:41087800-41098200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr19:41087800-41100000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr19:41088400-41092600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr19:41088400-41092600	Weak transcription	Colon Smooth Muscle	Colon

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