Variant report

Variant	rs3799842
Chromosome Location	chr6:109793029-109793030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109792133..109794693-chr6:109801926..109805583,3	MCF-7	breast:
2	chr6:109764609..109767226-chr6:109791352..109794243,2	K562	blood:
3	chr6:109786175..109787997-chr6:109790451..109793066,2	K562	blood:

Variant related genes	Relation type
ENSG00000112365	Chromatin interaction
ENSG00000135596	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10457192	0.84[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap]
rs10457194	0.83[CEU][hapmap]
rs10457195	0.84[CEU][hapmap]
rs1046943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054607	0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.91[MKK][hapmap];0.85[YRI][hapmap];0.92[ASN][1000 genomes]
rs1074765	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs1074766	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs10872033	0.83[EUR][1000 genomes]
rs11153183	0.84[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap]
rs11251	0.92[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap]
rs11754455	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs11755641	0.84[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap]
rs12194061	0.83[CEU][hapmap]
rs12197180	0.84[CEU][hapmap]
rs12198938	0.84[CEU][hapmap]
rs12199154	0.84[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap]
rs12212476	0.83[CEU][hapmap]
rs12214147	0.83[EUR][1000 genomes]
rs12529733	1.00[CEU][hapmap];0.84[YRI][hapmap]
rs13201430	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1321207	0.84[LWK][hapmap]
rs13220915	0.84[CEU][hapmap]
rs1406899	0.84[CEU][hapmap]
rs1476387	0.85[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17070591	0.96[CEU][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs17070656	0.80[YRI][hapmap]
rs1980591	0.83[CEU][hapmap]
rs2024850	0.84[CEU][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap]
rs2024853	0.84[CEU][hapmap]
rs2076929	0.80[YRI][hapmap]
rs2236084	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277113	0.96[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2277114	0.84[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap]
rs2884037	0.96[CEU][hapmap]
rs35146243	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35260632	0.83[AMR][1000 genomes]
rs3734652	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757235	0.96[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.80[YRI][hapmap]
rs3778474	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs3778478	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3899233	0.84[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap]
rs4636056	0.83[EUR][1000 genomes]
rs4945831	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4946967	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs4946976	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6568587	0.80[YRI][hapmap]
rs6911838	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs6920372	0.96[CEU][hapmap];0.80[YRI][hapmap]
rs6920712	0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.95[MKK][hapmap];0.85[YRI][hapmap];0.92[ASN][1000 genomes]
rs6925005	0.84[LWK][hapmap];0.80[YRI][hapmap]
rs6939548	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729888	0.84[CEU][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap]
rs730089	0.96[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.80[YRI][hapmap]
rs7356790	0.84[LWK][hapmap];0.80[YRI][hapmap]
rs736830	0.96[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.80[YRI][hapmap]
rs7748669	0.92[CEU][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs7751582	0.83[EUR][1000 genomes]
rs7754650	0.92[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap]
rs7755941	0.84[CEU][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap]
rs7768973	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7773950	0.84[CEU][hapmap]
rs910730	0.92[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9320286	0.80[EUR][1000 genomes]
rs9372213	0.85[GIH][hapmap]
rs9398202	0.81[CEU][hapmap];0.86[AMR][1000 genomes]
rs9400284	0.87[ASN][1000 genomes]
rs9400287	0.83[ASN][1000 genomes]
rs9480947	0.96[CEU][hapmap];0.80[YRI][hapmap]
rs9480956	0.96[CEU][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs9480958	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9487070	0.96[CEU][hapmap]
rs9487103	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[TSI][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs974034	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap]
rs9791241	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3799842	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs3799842	AKD1	cis	parietal	SCAN
rs3799842	MICAL1	cis	Artery Tibial	GTEx
rs3799842	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs3799842	AKD1	cis	cerebellum	SCAN
rs3799842	SMPD2	cis	parietal	SCAN
rs3799842	FIG4	cis	cerebellum	SCAN
rs3799842	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs3799842	CD164	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109778800-109798800	Weak transcription	Small Intestine	intestine
2	chr6:109780600-109800400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:109781400-109802200	Strong transcription	HSMM	muscle
4	chr6:109782000-109798800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr6:109782000-109799000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:109782400-109797600	Strong transcription	Dnd41	blood
7	chr6:109782400-109797800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:109782400-109798000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:109782400-109798200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:109782400-109798800	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr6:109782400-109798800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:109782400-109798800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:109782400-109798800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:109782400-109799000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:109782400-109799000	Strong transcription	Placenta	Placenta
16	chr6:109782400-109799200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr6:109782400-109799800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr6:109782400-109799800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr6:109782400-109800000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:109782400-109803000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:109782600-109797800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:109782600-109799600	Strong transcription	Fetal Muscle Trunk	muscle
23	chr6:109782600-109800000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:109783000-109797800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:109783000-109798000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:109783000-109798200	Strong transcription	Adipose Nuclei	Adipose
27	chr6:109783200-109799800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr6:109783600-109799000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:109785000-109794000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:109785200-109794800	Strong transcription	HMEC	breast
31	chr6:109785200-109796800	Strong transcription	Liver	Liver
32	chr6:109785600-109797800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:109785600-109798200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:109785600-109799200	Strong transcription	Primary hematopoietic stem cells	blood
35	chr6:109785800-109793200	Strong transcription	A549	lung
36	chr6:109785800-109796400	Strong transcription	Primary T cells from cord blood	blood
37	chr6:109785800-109798800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
38	chr6:109786000-109794600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr6:109786000-109797800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:109786200-109797000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:109786200-109797600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:109786200-109798200	Strong transcription	Osteobl	bone
43	chr6:109786200-109800200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:109786400-109799600	Strong transcription	Fetal Muscle Leg	muscle
45	chr6:109786600-109795000	Strong transcription	NHEK	skin
46	chr6:109786600-109799200	Strong transcription	Fetal Stomach	stomach
47	chr6:109786800-109794400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr6:109786800-109795200	Strong transcription	Spleen	Spleen
49	chr6:109786800-109795400	Strong transcription	Ovary	ovary
50	chr6:109786800-109795800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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