Variant report

Variant	rs12524639
Chromosome Location	chr6:109709459-109709460
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109706394..109711073-chr6:109716163..109719392,4	K562	blood:
2	chr6:109701817..109708859-chr6:109709273..109715844,12	K562	blood:
3	chr6:109703167..109707934-chr6:109708161..109712915,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMPD2-4	chr6:109709376-109709628	NONHSAT114399

Variant related genes	Relation type
ENSG00000135535	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10080429	0.92[EUR][1000 genomes]
rs1040284	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10457190	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10457194	0.86[CHB][hapmap]
rs10457195	0.86[CHB][hapmap]
rs1048203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10782161	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10782162	0.95[CEU][hapmap];0.81[CHB][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10872032	0.93[EUR][1000 genomes]
rs10872034	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11153171	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs11153174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11153175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11153176	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11153177	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11153180	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11153181	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11153183	0.86[CHB][hapmap]
rs11251	0.84[YRI][hapmap]
rs11753645	0.81[CEU][hapmap]
rs11754455	0.86[CHB][hapmap]
rs11755641	0.86[CHB][hapmap]
rs11967108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12190920	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12190996	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12192847	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12193493	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12194061	0.86[CHB][hapmap]
rs12197114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12197180	0.86[CHB][hapmap]
rs12198938	0.86[CHB][hapmap]
rs12199154	0.86[CHB][hapmap]
rs12206928	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12208933	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs12209691	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12212476	0.86[CHB][hapmap]
rs12213313	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12524273	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12528712	0.85[CEU][hapmap]
rs12528822	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13195517	0.85[CEU][hapmap]
rs13199519	0.86[CEU][hapmap]
rs13203252	0.84[CEU][hapmap]
rs13212766	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220915	0.86[CHB][hapmap]
rs1322816	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1358997	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1358998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1406899	0.86[CHB][hapmap]
rs1546980	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1590306	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17070580	0.95[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs1923725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2024850	0.86[CHB][hapmap]
rs2236582	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2275650	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277114	0.86[CHB][hapmap]
rs34202013	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35056702	0.93[EUR][1000 genomes]
rs36035949	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36099706	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778474	0.86[YRI][hapmap]
rs3778475	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778477	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3799835	0.82[CEU][hapmap]
rs3799839	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3807005	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3818934	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59056467	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59906308	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68042406	0.84[EUR][1000 genomes]
rs6911838	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs6920962	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs6929023	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7372	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs752262	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7754650	0.95[YRI][hapmap]
rs7755941	0.90[CHB][hapmap]
rs7773095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773950	0.86[CHB][hapmap]
rs9320287	0.95[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs9480933	0.93[EUR][1000 genomes]
rs9480948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480951	0.93[EUR][1000 genomes]
rs9480953	0.95[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs9480955	0.93[EUR][1000 genomes]
rs9480957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487068	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9487094	0.95[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs9487095	0.93[EUR][1000 genomes]
rs9487097	0.88[EUR][1000 genomes]
rs9487098	0.89[EUR][1000 genomes]
rs9487100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9885646	0.95[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12524639	SMPD2	cis	Whole Blood	GTEx
rs12524639	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs12524639	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs12524639	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs12524639	RP11-425D10.10	cis	Esophagus Mucosa	GTEx

Chromatin state (count:53 , 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	chr6:109706200-109710600	Weak transcription	HMEC	breast
11	chr6:109706200-109710800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:109706200-109711000	Weak transcription	Brain Anterior Caudate	brain
13	chr6:109706200-109711000	Weak transcription	Psoas Muscle	Psoas
14	chr6:109706200-109711600	Weak transcription	Fetal Lung	lung
15	chr6:109706200-109711800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:109706200-109717200	Weak transcription	Brain Angular Gyrus	brain
17	chr6:109706200-109717800	Weak transcription	Thymus	Thymus
18	chr6:109706400-109710600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:109706400-109710800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:109706400-109710800	Weak transcription	Brain Substantia Nigra	brain
21	chr6:109706400-109711400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr6:109706400-109715000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:109706400-109718400	Weak transcription	Primary B cells from cord blood	blood
24	chr6:109706600-109710800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:109706600-109710800	Weak transcription	Adipose Nuclei	Adipose
26	chr6:109706600-109711400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:109706600-109711600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:109706600-109711600	Weak transcription	Fetal Stomach	stomach
29	chr6:109706600-109714800	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:109706600-109717400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:109706600-109735800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:109706800-109710800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:109706800-109711400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr6:109706800-109711600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:109706800-109711600	Weak transcription	Pancreas	Pancrea
36	chr6:109706800-109711600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr6:109706800-109712600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:109706800-109715600	Weak transcription	Gastric	stomach
39	chr6:109706800-109718600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr6:109707000-109710800	Weak transcription	Stomach Mucosa	stomach
41	chr6:109707000-109711200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr6:109707000-109711600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:109707000-109712000	Weak transcription	Hela-S3	cervix
44	chr6:109707000-109755400	Weak transcription	Fetal Intestine Small	intestine
45	chr6:109707200-109710200	Weak transcription	Fetal Intestine Large	intestine
46	chr6:109707600-109710800	Weak transcription	Placenta	Placenta
47	chr6:109707800-109710800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:109708400-109710400	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr6:109709000-109709800	Enhancers	NHEK	skin
50	chr6:109709000-109710800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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