Variant report

Variant	rs7254601
Chromosome Location	chr19:36147315-36147316
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36110588..36113129-chr19:36146475..36149115,2	K562	blood:
2	chr19:36141764..36144285-chr19:36146929..36148660,2	K562	blood:
3	chr19:36137883..36140667-chr19:36145148..36147341,4	K562	blood:
4	chr19:36133838..36136832-chr19:36145196..36147862,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105672	Chromatin interaction
ENSG00000126267	Chromatin interaction
ENSG00000249115	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10413852	0.82[JPT][hapmap]
rs12461285	0.82[JPT][hapmap]
rs28633929	0.82[JPT][hapmap];0.81[TSI][hapmap]
rs2871921	0.82[JPT][hapmap]
rs3848662	0.82[JPT][hapmap]
rs62109998	0.83[AFR][1000 genomes]
rs8106959	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh 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	107 gene(s)	inside rSNPs	diseases
4	nsv543995	chr19:36139204-36203592	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7254601	U2AF1L4	Cis_1M	lymphoblastoid	RTeQTL
rs7254601	TMEM149	cis	multi-tissue	Pritchard
rs7254601	U2AF1L4	cis	Muscle Skeletal	GTEx
rs7254601	OR6Q1	trans	parietal	SCAN
rs7254601	ZNF568	cis	cerebellum	SCAN
rs7254601	TMEM149	Cis_1M	lymphoblastoid	RTeQTL
rs7254601	U2AF1L4	cis	Artery Tibial	GTEx
rs7254601	UPK1A	trans	cerebellum	SCAN
rs7254601	EIF3K	cis	parietal	SCAN
rs7254601	U2AF1L4	cis	Whole Blood	GTEx
rs7254601	RN7SL765P	cis	Muscle Skeletal	GTEx
rs7254601	COX6B1	cis	Artery Tibial	GTEx
rs7254601	ZNF233	cis	parietal	SCAN
rs7254601	CNFN	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36140000-36147800	Weak transcription	Aorta	Aorta
2	chr19:36140000-36148800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:36140000-36154000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:36140200-36152800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:36140400-36149200	Weak transcription	Small Intestine	intestine
6	chr19:36140400-36151600	Weak transcription	Stomach Mucosa	stomach
7	chr19:36140400-36164000	Weak transcription	Right Atrium	heart
8	chr19:36140600-36150400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:36140600-36153800	Strong transcription	Fetal Intestine Small	intestine
10	chr19:36140600-36157200	Strong transcription	Fetal Stomach	stomach
11	chr19:36140800-36153800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:36141000-36155600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr19:36141000-36157000	Strong transcription	Fetal Muscle Trunk	muscle
14	chr19:36141400-36156800	Strong transcription	Spleen	Spleen
15	chr19:36141400-36157200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:36141600-36151200	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr19:36141600-36152600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr19:36141800-36150200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr19:36141800-36151200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:36141800-36152800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr19:36141800-36153000	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr19:36141800-36154000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr19:36141800-36156800	Strong transcription	Fetal Thymus	thymus
24	chr19:36142000-36151200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:36142000-36151400	Strong transcription	Lung	lung
26	chr19:36142000-36152200	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr19:36142200-36151200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:36142200-36156800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:36142200-36156800	Strong transcription	Left Ventricle	heart
30	chr19:36142200-36157800	Weak transcription	Fetal Heart	heart
31	chr19:36142400-36152800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr19:36142800-36152800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:36142800-36157200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:36143000-36153800	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr19:36143600-36156000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:36144400-36156800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr19:36144600-36149600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:36144600-36149800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr19:36144600-36150200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr19:36144600-36150200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr19:36144600-36150200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:36144600-36150800	Strong transcription	Liver	Liver
43	chr19:36144600-36151000	Strong transcription	Dnd41	blood
44	chr19:36144600-36151200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:36144600-36151200	Strong transcription	Adipose Nuclei	Adipose
46	chr19:36144600-36151200	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr19:36144600-36151200	Strong transcription	A549	lung
48	chr19:36144600-36152200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:36144600-36152600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr19:36144600-36152800	Strong transcription	Monocytes-CD14+_RO01746	blood

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