Variant report

Variant	rs11670988
Chromosome Location	chr19:40886993-40886994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40886017..40887582-chr19:40898990..40901198,2	MCF-7	breast:
2	chr19:40886633..40888695-chr19:40900578..40902251,2	K562	blood:
3	chr19:40883373..40885815-chr19:40885950..40888263,2	K562	blood:
4	chr19:40878019..40881600-chr19:40884550..40887494,4	K562	blood:
5	chr19:40878611..40882541-chr19:40884534..40888641,8	K562	blood:
6	chr19:40884158..40887666-chr19:40907881..40910948,4	K562	blood:

Variant related genes	Relation type
ENSG00000105223	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11672523	1.00[ASW][hapmap]
rs7258698	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer 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 miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv911707	chr19:40855255-40948202	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11670988	ZNF233	cis	cerebellum	SCAN
rs11670988	MARK4	cis	parietal	SCAN
rs11670988	STRN4	cis	cerebellum	SCAN
rs11670988	BCL3	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40872200-40887000	Strong transcription	Liver	Liver
2	chr19:40872200-40887400	Weak transcription	Primary B cells from cord blood	blood
3	chr19:40872200-40887400	Weak transcription	Stomach Mucosa	stomach
4	chr19:40872800-40904400	Weak transcription	Right Atrium	heart
5	chr19:40873000-40887000	Strong transcription	Primary T cells from cord blood	blood
6	chr19:40873000-40887000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:40873000-40887400	Strong transcription	Duodenum Smooth Muscle	Duodenum
8	chr19:40873000-40887800	Strong transcription	Stomach Smooth Muscle	stomach
9	chr19:40873400-40887200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:40873400-40887400	Strong transcription	Fetal Brain Female	brain
11	chr19:40873800-40887800	Strong transcription	Fetal Stomach	stomach
12	chr19:40873800-40890800	Weak transcription	Fetal Heart	heart
13	chr19:40874200-40887200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr19:40874400-40887400	Strong transcription	Brain Germinal Matrix	brain
15	chr19:40874600-40887400	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr19:40874600-40890200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr19:40875600-40887200	Strong transcription	Fetal Muscle Leg	muscle
18	chr19:40875800-40887000	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr19:40876200-40888200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr19:40876800-40887200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:40877400-40887400	Strong transcription	Fetal Intestine Small	intestine
22	chr19:40879000-40889000	Weak transcription	K562	blood
23	chr19:40879000-40898600	Weak transcription	NHEK	skin
24	chr19:40880400-40888000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr19:40880600-40887200	Weak transcription	Fetal Thymus	thymus
26	chr19:40880600-40889000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr19:40880800-40887000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr19:40880800-40889000	Weak transcription	HSMM	muscle
29	chr19:40880800-40890800	Weak transcription	HSMMtube	muscle
30	chr19:40881000-40888200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr19:40881200-40888400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:40881400-40887000	Strong transcription	Gastric	stomach
33	chr19:40882200-40887000	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr19:40882200-40887400	Strong transcription	Ovary	ovary
35	chr19:40882400-40887000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:40882400-40887000	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr19:40882400-40887200	Strong transcription	Lung	lung
38	chr19:40883000-40887600	Weak transcription	Osteobl	bone
39	chr19:40883600-40887200	Strong transcription	Colonic Mucosa	Colon
40	chr19:40884000-40887200	Weak transcription	Brain Substantia Nigra	brain
41	chr19:40884400-40887400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr19:40884600-40887000	Strong transcription	Adipose Nuclei	Adipose
43	chr19:40884800-40889000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:40884800-40889600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:40884800-40891000	Weak transcription	A549	lung
46	chr19:40885000-40888400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:40885000-40888600	Weak transcription	Left Ventricle	heart
48	chr19:40885000-40889600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr19:40885000-40889600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr19:40885000-40889800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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