Variant report

Variant	rs7260127
Chromosome Location	chr19:19280499-19280500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19276342..19278695-chr19:19279109..19280933,2	K562	blood:
2	chr19:19280114..19282646-chr19:19429552..19431405,2	MCF-7	breast:
3	chr19:19279506..19282646-chr19:19302669..19304636,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064489	Chromatin interaction
ENSG00000105705	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000254901	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1005980	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10417796	0.83[EUR][1000 genomes]
rs10418053	0.96[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs1050544	0.96[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs10854008	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10854009	0.82[EUR][1000 genomes]
rs10854012	0.88[ASW][hapmap];1.00[CEU][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11669408	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11669860	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11669861	0.88[EUR][1000 genomes]
rs12609573	1.00[CEU][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12972894	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12974672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975096	0.81[EUR][1000 genomes]
rs12975253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975290	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12980269	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12980955	0.84[EUR][1000 genomes]
rs12981160	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1858846	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2238668	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239369	0.88[ASW][hapmap];1.00[CEU][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2239370	0.96[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs2283623	0.84[EUR][1000 genomes]
rs2314035	0.83[EUR][1000 genomes]
rs35342977	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3787040	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808185	0.81[EUR][1000 genomes]
rs539	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62135499	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71332145	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250650	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7256811	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72997174	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs741706	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8101388	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7260127	C19orf50	cis	parietal	SCAN
rs7260127	RAB8A	cis	parietal	SCAN
rs7260127	C19orf50	cis	cerebellum	SCAN
rs7260127	PDE4C	cis	cerebellum	SCAN
rs7260127	ZNF682	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19249600-19282600	Weak transcription	NHLF	lung
2	chr19:19249800-19280600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:19258400-19280600	Weak transcription	Right Ventricle	heart
4	chr19:19259000-19290200	Weak transcription	Colon Smooth Muscle	Colon
5	chr19:19260200-19280600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr19:19260200-19280600	Weak transcription	Brain Hippocampus Middle	brain
7	chr19:19260400-19280800	Weak transcription	Ovary	ovary
8	chr19:19260600-19281000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr19:19260800-19280800	Weak transcription	Liver	Liver
10	chr19:19264200-19280800	Weak transcription	HSMMtube	muscle
11	chr19:19267200-19280800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr19:19268000-19280600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr19:19268000-19280600	Weak transcription	Primary T cells from cord blood	blood
14	chr19:19268000-19280600	Weak transcription	Adipose Nuclei	Adipose
15	chr19:19268200-19282600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:19268400-19280600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr19:19268400-19280800	Weak transcription	Fetal Lung	lung
18	chr19:19268800-19287200	Weak transcription	Dnd41	blood
19	chr19:19269000-19281000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr19:19271800-19281000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr19:19274000-19280600	Weak transcription	Fetal Thymus	thymus
22	chr19:19277400-19300600	Weak transcription	Small Intestine	intestine
23	chr19:19277800-19280600	Weak transcription	NHEK	skin
24	chr19:19278800-19280600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr19:19279200-19280600	Weak transcription	Fetal Stomach	stomach
26	chr19:19280200-19281800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr19:19280200-19281800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
28	chr19:19280400-19280600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
29	chr19:19280400-19280600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
30	chr19:19280400-19280600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:19280400-19280600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr19:19280400-19280600	Enhancers	Primary B cells from cord blood	blood
33	chr19:19280400-19280600	Enhancers	Brain Angular Gyrus	brain
34	chr19:19280400-19280600	Enhancers	Brain Cingulate Gyrus	brain
35	chr19:19280400-19280600	Bivalent Enhancer	Colonic Mucosa	Colon
36	chr19:19280400-19280600	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr19:19280400-19280600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
38	chr19:19280400-19280600	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr19:19280400-19280600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr19:19280400-19280600	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr19:19280400-19280600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
42	chr19:19280400-19280600	Enhancers	K562	blood
43	chr19:19280400-19280800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
44	chr19:19280400-19280800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
45	chr19:19280400-19280800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr19:19280400-19280800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr19:19280400-19280800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:19280400-19280800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:19280400-19280800	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr19:19280400-19280800	Bivalent Enhancer	Fetal Muscle Leg	muscle

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