Variant report

Variant	rs9487100
Chromosome Location	chr6:109750410-109750411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109750346..109753133-chr6:109776216..109778124,3	K562	blood:
2	chr6:109747081..109748999-chr6:109749255..109751645,2	MCF-7	breast:
3	chr6:109702791..109704639-chr6:109749211..109751397,2	MCF-7	breast:
4	chr6:109740450..109742532-chr6:109747741..109750415,2	MCF-7	breast:
5	chr6:109744870..109747846-chr6:109748398..109750532,2	K562	blood:
6	chr6:109747606..109757389-chr6:109757828..109761794,11	K562	blood:

Variant related genes	Relation type
ENSG00000260273	Chromatin interaction
ENSG00000135596	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000185250	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10080429	0.95[EUR][1000 genomes]
rs1040284	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10457190	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[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];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10499053	0.95[CEU][hapmap]
rs10782161	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782162	0.95[CEU][hapmap];0.80[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10872032	0.92[EUR][1000 genomes]
rs10872034	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11153171	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs11153174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11153175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11153176	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11153177	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153180	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153181	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153183	0.86[CHB][hapmap]
rs11753645	0.81[CEU][hapmap]
rs11754455	0.85[CHB][hapmap]
rs11755641	0.86[CHB][hapmap]
rs11967108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12190920	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12190996	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12192847	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12193493	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12194061	0.86[CHB][hapmap]
rs12197114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197180	0.86[CHB][hapmap]
rs12198938	0.86[CHB][hapmap]
rs12199154	0.86[CHB][hapmap]
rs12206928	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12208933	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs12209691	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12212476	0.86[CHB][hapmap]
rs12213313	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12524273	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12524639	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]
rs12528712	0.85[CEU][hapmap]
rs12528822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13195517	0.85[CEU][hapmap]
rs13199519	0.85[CEU][hapmap]
rs13203252	0.84[CEU][hapmap]
rs13212766	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13220915	0.85[CHB][hapmap]
rs1322816	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1358997	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1358998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1406899	0.86[CHB][hapmap]
rs1546980	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1590306	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17070580	0.95[CEU][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs1923725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1980591	0.85[CHB][hapmap]
rs2024850	0.86[CHB][hapmap]
rs2236582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2275650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277114	0.86[CHB][hapmap]
rs34202013	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35056702	0.95[EUR][1000 genomes]
rs36035949	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36099706	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778475	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778477	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3799835	0.81[CEU][hapmap]
rs3799839	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3807005	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3818934	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59056467	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59906308	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68042406	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6911838	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs6914498	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs6920962	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs6929023	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7372	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs752262	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7755941	0.90[CHB][hapmap]
rs7773095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7773950	0.86[CHB][hapmap]
rs9320287	0.95[CEU][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs9480933	0.91[EUR][1000 genomes]
rs9480948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9480951	0.95[EUR][1000 genomes]
rs9480953	0.95[CEU][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes]
rs9480955	0.95[EUR][1000 genomes]
rs9480957	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]
rs9487068	0.94[EUR][1000 genomes]
rs9487094	0.95[CEU][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs9487095	0.95[EUR][1000 genomes]
rs9487097	0.91[EUR][1000 genomes]
rs9487098	0.92[EUR][1000 genomes]
rs9885646	0.95[CEU][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9487100	SMPD2	cis	Whole Blood	GTEx
rs9487100	SMPD2	cis	multi-tissue	Pritchard
rs9487100	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs9487100	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs9487100	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs9487100	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109707000-109755400	Weak transcription	Fetal Intestine Small	intestine
2	chr6:109721200-109760600	Weak transcription	Fetal Brain Female	brain
3	chr6:109725800-109760800	Weak transcription	Brain Anterior Caudate	brain
4	chr6:109736600-109760800	Weak transcription	Brain Angular Gyrus	brain
5	chr6:109740400-109754800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:109745600-109760800	Weak transcription	Gastric	stomach
7	chr6:109745800-109750800	Weak transcription	Left Ventricle	heart
8	chr6:109746000-109753400	Weak transcription	Pancreas	Pancrea
9	chr6:109746400-109750600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:109746400-109750600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:109746400-109750600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:109746600-109750800	Weak transcription	NHEK	skin
13	chr6:109749600-109753800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:109750000-109750600	Enhancers	Fetal Lung	lung
15	chr6:109750000-109751000	Enhancers	Brain Hippocampus Middle	brain
16	chr6:109750000-109751000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr6:109750000-109751000	Enhancers	HUVEC	blood vessel
18	chr6:109750200-109750600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:109750200-109750600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:109750200-109750600	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr6:109750200-109750600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr6:109750200-109750600	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr6:109750200-109750600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr6:109750200-109750600	Active TSS	Stomach Smooth Muscle	stomach
25	chr6:109750200-109750600	Flanking Active TSS	Hela-S3	cervix
26	chr6:109750200-109750800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:109750200-109750800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:109750200-109751200	Enhancers	Fetal Muscle Leg	muscle
29	chr6:109750200-109751400	Enhancers	Fetal Stomach	stomach
30	chr6:109750400-109750600	Active TSS	Rectal Smooth Muscle	rectum
31	chr6:109750400-109750800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:109750400-109750800	Enhancers	Ovary	ovary
33	chr6:109750400-109750800	Active TSS	Osteobl	bone
34	chr6:109750400-109751000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:109750400-109751000	Enhancers	Psoas Muscle	Psoas

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