Variant report

Variant	rs13199519
Chromosome Location	chr6:109709175-109709176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109517222..109519180-chr6:109707753..109709396,2	MCF-7	breast:
2	chr6:109706394..109711073-chr6:109716163..109719392,4	K562	blood:
3	chr6:109703167..109707934-chr6:109708161..109712915,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135535	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1048203	0.90[CEU][hapmap]
rs10499052	0.94[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap]
rs10782162	0.90[CEU][hapmap]
rs11153174	0.81[YRI][hapmap]
rs11753645	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11757877	0.84[CHB][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12524502	0.85[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12524639	0.86[CEU][hapmap]
rs12528566	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12528712	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12528822	0.90[CEU][hapmap]
rs13192476	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13195517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13203252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13220304	0.89[CEU][hapmap]
rs1322818	0.81[CEU][hapmap];0.86[AMR][1000 genomes]
rs1358998	0.90[CEU][hapmap]
rs17070580	0.85[CEU][hapmap]
rs2236582	0.84[CEU][hapmap]
rs2275650	0.90[CEU][hapmap];0.83[YRI][hapmap]
rs2275652	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34131679	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34292461	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34320275	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35452836	0.84[EUR][1000 genomes]
rs35969918	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3757238	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3799835	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799840	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4428538	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61076041	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61233650	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61318425	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67857472	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6911838	0.81[CEU][hapmap]
rs6929208	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7773095	0.90[CEU][hapmap]
rs9320287	0.85[CEU][hapmap]
rs9480948	0.90[CEU][hapmap]
rs9480953	0.81[CEU][hapmap]
rs9480957	0.90[CEU][hapmap]
rs9487094	0.84[CEU][hapmap]
rs9487100	0.85[CEU][hapmap]
rs9885646	0.85[CEU][hapmap]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13199519	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs13199519	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs13199519	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs13199519	SMPD2	cis	Whole Blood	GTEx
rs13199519	MICAL1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109704600-109710800	Weak transcription	Aorta	Aorta
2	chr6:109705000-109745200	Weak transcription	Fetal Kidney	kidney
3	chr6:109705200-109710800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr6:109705400-109710800	Weak transcription	Right Atrium	heart
5	chr6:109705800-109711000	Weak transcription	Primary T cells from cord blood	blood
6	chr6:109705800-109711000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:109706000-109710800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:109706000-109710800	Weak transcription	Left Ventricle	heart
9	chr6:109706000-109711600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:109706200-109709200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:109706200-109709200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:109706200-109710600	Weak transcription	HMEC	breast
13	chr6:109706200-109710800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:109706200-109711000	Weak transcription	Brain Anterior Caudate	brain
15	chr6:109706200-109711000	Weak transcription	Psoas Muscle	Psoas
16	chr6:109706200-109711600	Weak transcription	Fetal Lung	lung
17	chr6:109706200-109711800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:109706200-109717200	Weak transcription	Brain Angular Gyrus	brain
19	chr6:109706200-109717800	Weak transcription	Thymus	Thymus
20	chr6:109706400-109710600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:109706400-109710800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:109706400-109710800	Weak transcription	Brain Substantia Nigra	brain
23	chr6:109706400-109711400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr6:109706400-109715000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:109706400-109718400	Weak transcription	Primary B cells from cord blood	blood
26	chr6:109706600-109710800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:109706600-109710800	Weak transcription	Adipose Nuclei	Adipose
28	chr6:109706600-109711400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:109706600-109711600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr6:109706600-109711600	Weak transcription	Fetal Stomach	stomach
31	chr6:109706600-109714800	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:109706600-109717400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:109706600-109735800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:109706800-109710800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:109706800-109711400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr6:109706800-109711600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:109706800-109711600	Weak transcription	Pancreas	Pancrea
38	chr6:109706800-109711600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr6:109706800-109712600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:109706800-109715600	Weak transcription	Gastric	stomach
41	chr6:109706800-109718600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr6:109707000-109710800	Weak transcription	Stomach Mucosa	stomach
43	chr6:109707000-109711200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr6:109707000-109711600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr6:109707000-109712000	Weak transcription	Hela-S3	cervix
46	chr6:109707000-109755400	Weak transcription	Fetal Intestine Small	intestine
47	chr6:109707200-109710200	Weak transcription	Fetal Intestine Large	intestine
48	chr6:109707600-109710800	Weak transcription	Placenta	Placenta
49	chr6:109707800-109710800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:109708400-109710400	Enhancers	Primary neutrophils fromperipheralblood	blood

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