Variant report

Variant	rs415499
Chromosome Location	chr19:44490024-44490025
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44486769..44491037-chr19:44505585..44508395,4	MCF-7	breast:
2	chr19:44487777..44490285-chr19:44555817..44558004,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159882	Chromatin interaction
ENSG00000178386	Chromatin interaction
ENSG00000266921	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs384596	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs390784	0.96[CEU][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs397276	0.82[CHB][hapmap]
rs397706	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs398981	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs425530	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs430746	0.96[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes]
rs55821779	0.80[EUR][1000 genomes]
rs56053925	0.80[EUR][1000 genomes]
rs7255894	0.81[JPT][hapmap]
rs8099924	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv579854	chr19:44411543-44490024	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv912109	chr19:44459074-44493142	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs415499	KLK6	cis	parietal	SCAN
rs415499	RP11-15A1.7	cis	Whole Blood	GTEx
rs415499	ZNF155	cis	Whole Blood	GTEx
rs415499	ZNF175	cis	cerebellum	SCAN
rs415499	FOXA3	cis	cerebellum	SCAN
rs415499	ZNF155	cis	lymphoblastoid	seeQTL
rs415499	ZNF528	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44489000-44493600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:44489200-44490200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:44489200-44490200	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr19:44489200-44490200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:44489200-44490200	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr19:44489200-44490200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr19:44489200-44490200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr19:44489200-44490200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr19:44489200-44490200	Enhancers	Fetal Brain Male	brain
10	chr19:44489200-44490200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr19:44489200-44490400	Enhancers	Fetal Heart	heart
12	chr19:44489200-44491600	Weak transcription	Aorta	Aorta
13	chr19:44489200-44492400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr19:44489200-44492400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr19:44489200-44492600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:44489200-44492600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr19:44489200-44492600	Weak transcription	Fetal Muscle Leg	muscle
18	chr19:44489200-44492600	Weak transcription	Psoas Muscle	Psoas
19	chr19:44489200-44493000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr19:44489200-44493200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:44489200-44493200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:44489200-44493400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:44489200-44493400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:44489200-44493400	Weak transcription	Brain Angular Gyrus	brain
25	chr19:44489200-44493400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:44489200-44493600	Weak transcription	Colonic Mucosa	Colon
27	chr19:44489200-44494600	Weak transcription	Gastric	stomach
28	chr19:44489200-44494600	Weak transcription	NHLF	lung
29	chr19:44489200-44496000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:44489200-44496000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:44489200-44496000	Weak transcription	Small Intestine	intestine
32	chr19:44489200-44496600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr19:44489200-44500400	Weak transcription	HUVEC	blood vessel
34	chr19:44489200-44506200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr19:44489200-44506200	Weak transcription	Hela-S3	cervix
36	chr19:44489400-44490200	Enhancers	GM12878-XiMat	blood
37	chr19:44489400-44491000	Weak transcription	Fetal Lung	lung
38	chr19:44489400-44491800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:44489400-44492000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:44489400-44492000	Weak transcription	Colon Smooth Muscle	Colon
41	chr19:44489400-44492200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr19:44489400-44492400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:44489400-44492400	Weak transcription	Pancreas	Pancrea
44	chr19:44489400-44492400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr19:44489400-44492400	Weak transcription	HSMM	muscle
46	chr19:44489400-44492600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:44489400-44492600	Weak transcription	Brain Germinal Matrix	brain
48	chr19:44489400-44492600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr19:44489400-44492600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr19:44489400-44492600	Weak transcription	Stomach Smooth Muscle	stomach

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