Variant report

Variant	rs6911838
Chromosome Location	chr6:109799923-109799924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109771720..109774696-chr6:109798404..109799936,2	MCF-7	breast:
2	chr6:109764918..109767515-chr6:109797927..109799949,2	MCF-7	breast:
3	chr6:109766673..109769201-chr6:109798430..109801986,3	MCF-7	breast:
4	chr6:109783085..109784938-chr6:109797563..109800257,2	K562	blood:
5	chr6:109417075..109418905-chr6:109799494..109801799,2	K562	blood:
6	chr6:109702682..109704244-chr6:109798920..109800659,2	K562	blood:
7	chr6:109785634..109787468-chr6:109799694..109802286,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135535	Chromatin interaction
ENSG00000135596	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1040284	0.80[EUR][1000 genomes]
rs1046943	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs1048203	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs10499053	0.90[CEU][hapmap]
rs1054607	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs10782161	0.84[EUR][1000 genomes]
rs10782162	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs10872034	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11153171	0.91[CEU][hapmap];0.80[CHB][hapmap];0.81[EUR][1000 genomes]
rs11153174	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs11153175	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs11153176	0.80[EUR][1000 genomes]
rs11153177	0.84[EUR][1000 genomes]
rs11153180	0.84[EUR][1000 genomes]
rs11153181	0.84[EUR][1000 genomes]
rs11251	0.84[CHB][hapmap]
rs11967108	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs12190920	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12190996	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12192847	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12193493	0.80[EUR][1000 genomes]
rs12197114	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs12208933	0.91[CEU][hapmap]
rs12209691	0.92[EUR][1000 genomes]
rs12213313	0.84[EUR][1000 genomes]
rs12524273	0.82[EUR][1000 genomes]
rs12524639	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs12528712	0.81[CEU][hapmap]
rs12528822	0.95[CEU][hapmap]
rs13195517	0.81[CEU][hapmap]
rs13199519	0.81[CEU][hapmap]
rs13201430	0.90[CHB][hapmap]
rs1321328	0.91[CEU][hapmap]
rs1322816	0.81[EUR][1000 genomes]
rs1358997	0.81[EUR][1000 genomes]
rs1358998	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs1476387	0.84[CHB][hapmap]
rs1546980	0.90[EUR][1000 genomes]
rs1590306	0.80[EUR][1000 genomes]
rs17070580	0.90[CEU][hapmap]
rs1923725	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs2236084	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs2236582	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs2275650	0.95[CEU][hapmap]
rs2277113	0.84[CHB][hapmap]
rs35146243	0.85[ASN][1000 genomes]
rs36035949	0.81[EUR][1000 genomes]
rs36099706	0.84[EUR][1000 genomes]
rs3734652	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs3757234	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs3778474	0.84[CHB][hapmap]
rs3778475	0.80[EUR][1000 genomes]
rs3778477	0.91[EUR][1000 genomes]
rs3778478	0.85[ASN][1000 genomes]
rs3799839	0.81[EUR][1000 genomes]
rs3799842	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs3807005	0.92[EUR][1000 genomes]
rs4946967	0.84[CHB][hapmap]
rs59906308	0.82[EUR][1000 genomes]
rs68042406	0.89[EUR][1000 genomes]
rs6914498	0.91[CEU][hapmap]
rs6920712	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs6920962	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs6929023	0.82[EUR][1000 genomes]
rs6939548	0.85[ASN][1000 genomes]
rs7372	0.80[EUR][1000 genomes]
rs752262	0.90[EUR][1000 genomes]
rs7748669	0.84[CHB][hapmap]
rs7754650	0.84[CHB][hapmap]
rs7773095	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs910730	0.84[CHB][hapmap]
rs9320287	0.90[CEU][hapmap]
rs9480948	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs9480953	0.91[CEU][hapmap]
rs9480957	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs9487094	0.90[CEU][hapmap]
rs9487100	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs971434	0.91[CEU][hapmap]
rs9791241	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs9885646	0.90[CEU][hapmap]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6911838	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs6911838	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs6911838	SMPD2	cis	multi-tissue	Pritchard
rs6911838	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs6911838	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs6911838	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109780600-109800400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:109781400-109802200	Strong transcription	HSMM	muscle
3	chr6:109782400-109800000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:109782400-109803000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:109782600-109800000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:109786200-109800200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:109787800-109800600	Weak transcription	Fetal Heart	heart
8	chr6:109789400-109803200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:109794400-109801200	Weak transcription	HSMMtube	muscle
10	chr6:109795000-109800000	Weak transcription	NH-A	brain
11	chr6:109795200-109802400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:109796800-109800000	Weak transcription	NHLF	lung
13	chr6:109797800-109800000	Genic enhancers	Brain Angular Gyrus	brain
14	chr6:109797800-109800200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:109797800-109803400	Transcr. at gene 5' and 3'	Dnd41	blood
16	chr6:109798000-109800000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:109798000-109800200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr6:109798000-109800200	Weak transcription	A549	lung
19	chr6:109798000-109803400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:109798000-109803400	Genic enhancers	Fetal Thymus	thymus
21	chr6:109798200-109800200	Weak transcription	Osteobl	bone
22	chr6:109798200-109802200	Weak transcription	Gastric	stomach
23	chr6:109798200-109803000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:109798400-109800200	Weak transcription	HMEC	breast
25	chr6:109798600-109800000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:109798600-109802600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr6:109798600-109802800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
28	chr6:109798600-109803400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
29	chr6:109798800-109800000	Enhancers	K562	blood
30	chr6:109798800-109800400	Genic enhancers	Brain Cingulate Gyrus	brain
31	chr6:109798800-109800600	Enhancers	Brain Germinal Matrix	brain
32	chr6:109798800-109800800	Enhancers	Stomach Mucosa	stomach
33	chr6:109798800-109801200	Enhancers	Adipose Nuclei	Adipose
34	chr6:109798800-109801200	Enhancers	Small Intestine	intestine
35	chr6:109798800-109801600	Enhancers	Right Atrium	heart
36	chr6:109798800-109802400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
37	chr6:109799000-109800000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
38	chr6:109799000-109800000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr6:109799000-109800400	Enhancers	Brain Substantia Nigra	brain
40	chr6:109799000-109800600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:109799000-109801800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:109799000-109801800	Weak transcription	Fetal Kidney	kidney
43	chr6:109799000-109803000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
44	chr6:109799200-109800000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:109799200-109800200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr6:109799200-109800200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr6:109799200-109800400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr6:109799200-109800400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:109799200-109800400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:109799200-109800400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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