Variant report

Variant	rs3799499
Chromosome Location	chr6:28354250-28354251
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28302573..28306599-chr6:28349951..28354470,6	K562	blood:
2	chr6:28352795..28355228-chr6:28357917..28359743,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1005126	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11751928	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11755387	0.90[CHB][hapmap]
rs13190937	0.88[ASW][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.83[LWK][hapmap];0.86[ASN][1000 genomes]
rs13193272	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13196606	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13199081	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13203055	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13209596	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13215804	0.88[ASW][hapmap];0.90[CHB][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs13217326	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1361385	0.88[ASW][hapmap]
rs16894011	0.90[CHB][hapmap]
rs16894091	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16894106	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16894116	0.80[CEU][hapmap]
rs16901847	0.80[CEU][hapmap]
rs17856167	0.90[CHB][hapmap]
rs2232427	0.90[CHB][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28505234	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3734563	0.88[ASW][hapmap]
rs3799500	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3800328	0.82[ASW][hapmap]
rs4357130	0.88[ASW][hapmap]
rs57071502	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58020991	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6902687	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6905380	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6907950	0.88[ASW][hapmap]
rs6908137	0.88[ASW][hapmap]
rs6931359	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6940744	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71559081	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7740429	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7750526	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7754960	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764722	0.88[ASW][hapmap]
rs7774981	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461458	0.88[ASW][hapmap]
rs9468355	0.83[ASW][hapmap]
rs9468356	0.82[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9468358	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9468364	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs9468370	0.88[ASW][hapmap]
rs9969098	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3799499	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs3799499	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs3799499	ZSCAN23	cis	Artery Tibial	GTEx
rs3799499	AL022393.7	cis	Muscle Skeletal	GTEx
rs3799499	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3799499	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3799499	AL022393.7	cis	Heart Left Ventricle	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28324400-28357200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:28324400-28357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:28324600-28358600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:28345000-28361600	Strong transcription	Dnd41	blood
5	chr6:28348400-28357800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:28350400-28357600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:28350400-28358200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:28350400-28358200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:28351200-28358000	Weak transcription	Small Intestine	intestine
10	chr6:28351200-28358200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:28351400-28354800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr6:28351400-28357000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:28351400-28357400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:28351600-28354800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:28351600-28355000	Weak transcription	Lung	lung
16	chr6:28351600-28355000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:28351600-28355000	Weak transcription	Thymus	Thymus
18	chr6:28351600-28355600	Weak transcription	Aorta	Aorta
19	chr6:28351600-28355600	Weak transcription	Placenta	Placenta
20	chr6:28351600-28355800	Weak transcription	Brain Substantia Nigra	brain
21	chr6:28351600-28357000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:28351600-28357200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:28351600-28357400	Weak transcription	Fetal Kidney	kidney
24	chr6:28351600-28357600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:28351600-28357600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:28351600-28357600	Weak transcription	Esophagus	oesophagus
27	chr6:28351600-28357600	Weak transcription	Pancreas	Pancrea
28	chr6:28351600-28358200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:28351600-28358200	Weak transcription	Fetal Brain Male	brain
30	chr6:28351600-28358200	Weak transcription	Right Ventricle	heart
31	chr6:28351600-28358200	Weak transcription	Spleen	Spleen
32	chr6:28351600-28358200	Weak transcription	HSMMtube	muscle
33	chr6:28351600-28358400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:28351600-28358400	Weak transcription	Colonic Mucosa	Colon
35	chr6:28351600-28358400	Weak transcription	Gastric	stomach
36	chr6:28351600-28358400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr6:28351600-28358400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr6:28351600-28358600	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr6:28351600-28358600	Weak transcription	Psoas Muscle	Psoas
40	chr6:28351600-28364600	Weak transcription	Right Atrium	heart
41	chr6:28351800-28354400	Weak transcription	Fetal Stomach	stomach
42	chr6:28351800-28354800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:28351800-28355000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:28351800-28355000	Weak transcription	Primary B cells from cord blood	blood
45	chr6:28351800-28355000	Weak transcription	Brain Hippocampus Middle	brain
46	chr6:28351800-28355000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr6:28351800-28355000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr6:28351800-28355000	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr6:28351800-28355200	Weak transcription	Left Ventricle	heart
50	chr6:28351800-28355400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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