Variant report

Variant	rs12460885
Chromosome Location	chr19:42536753-42536754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:42463311..42465601-chr19:42534138..42536977,3	K562	blood:
2	chr19:42527263..42533140-chr19:42533961..42538998,6	MCF-7	breast:
3	chr19:42535754..42538342-chr19:42542114..42544561,2	K562	blood:

Variant related genes	Relation type
ENSG00000105404	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11083643	1.00[LWK][hapmap]
rs11668239	1.00[LWK][hapmap]
rs11669918	1.00[LWK][hapmap]
rs11671088	1.00[LWK][hapmap]
rs12610025	1.00[LWK][hapmap]
rs12985559	1.00[LWK][hapmap]
rs2303797	1.00[LWK][hapmap]
rs28364793	1.00[LWK][hapmap]
rs34343924	1.00[LWK][hapmap]
rs3745226	1.00[LWK][hapmap]
rs9676263	1.00[LWK][hapmap]

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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS 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	13 gene(s)	inside rSNPs	diseases
5	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42511000-42542600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:42527200-42541800	Weak transcription	Aorta	Aorta
3	chr19:42528400-42553000	Weak transcription	Spleen	Spleen
4	chr19:42529400-42541600	Weak transcription	Brain Anterior Caudate	brain
5	chr19:42529600-42540800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr19:42529600-42541800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr19:42529800-42538200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:42529800-42541800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr19:42530200-42541200	Weak transcription	Fetal Heart	heart
10	chr19:42532000-42541800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:42533000-42536800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:42533000-42545800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:42533200-42536800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr19:42533200-42538600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr19:42534400-42539000	Enhancers	Adipose Nuclei	Adipose
16	chr19:42534600-42537000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:42534800-42538200	Weak transcription	Fetal Brain Male	brain
18	chr19:42535000-42537200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:42535000-42537400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:42535200-42537000	Enhancers	Fetal Brain Female	brain
21	chr19:42535200-42537200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:42535600-42537200	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr19:42535600-42538200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr19:42535600-42539800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr19:42535600-42540400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr19:42535600-42555200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr19:42535800-42540800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:42536000-42537000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:42536000-42537000	Enhancers	Colon Smooth Muscle	Colon
30	chr19:42536000-42537200	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr19:42536000-42537200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:42536000-42537200	Enhancers	Brain Hippocampus Middle	brain
33	chr19:42536000-42537400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:42536000-42537600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:42536000-42542000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr19:42536200-42537000	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr19:42536200-42537000	Enhancers	Duodenum Mucosa	Duodenum
38	chr19:42536200-42538200	Weak transcription	Fetal Muscle Leg	muscle
39	chr19:42536200-42540600	Weak transcription	Fetal Stomach	stomach
40	chr19:42536200-42541600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr19:42536400-42536800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr19:42536400-42537000	Enhancers	Fetal Kidney	kidney
43	chr19:42536400-42537200	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr19:42536400-42537200	Enhancers	Brain Germinal Matrix	brain
45	chr19:42536400-42539000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr19:42536600-42536800	Enhancers	Brain Angular Gyrus	brain
47	chr19:42536600-42537000	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr19:42536600-42537000	Enhancers	Brain Substantia Nigra	brain
49	chr19:42536600-42537200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr19:42536600-42540600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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