Variant report

Variant	rs12201356
Chromosome Location	chr6:110015875-110015876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10457195	0.81[EUR][1000 genomes]
rs10457203	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10782163	0.80[EUR][1000 genomes]
rs11153188	0.82[EUR][1000 genomes]
rs11153213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11153214	0.94[ASN][1000 genomes]
rs11153215	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11153216	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11752791	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11754340	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11755641	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12190372	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12191353	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12192268	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12192776	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12193719	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12194061	0.82[EUR][1000 genomes]
rs12194157	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12197838	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12197950	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12201444	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12203993	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12204548	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12205140	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12205485	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12208018	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12210706	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12214639	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12215077	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12528392	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12528781	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13191066	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13198852	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13199109	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13199135	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13201430	0.84[EUR][1000 genomes]
rs13201947	0.80[EUR][1000 genomes]
rs13201951	0.83[EUR][1000 genomes]
rs1322124	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1960325	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1980591	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2025147	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2025148	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2273752	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2357124	0.81[EUR][1000 genomes]
rs36131450	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3799845	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3799849	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3899233	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4141930	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4490694	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4945833	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4947016	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6568592	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6911700	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71541003	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs729888	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7341297	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7451512	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs749517	0.80[EUR][1000 genomes]
rs7767525	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv933105	chr6:109933270-110064342	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv604485	chr6:109959269-110054486	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12201356	SMPD2	cis	Whole Blood	GTEx
rs12201356	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs12201356	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs12201356	C6orf199	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:110013000-110022400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:110013000-110023600	Weak transcription	Gastric	stomach
4	chr6:110013000-110024800	Weak transcription	Lung	lung
5	chr6:110013000-110025200	Weak transcription	Small Intestine	intestine
6	chr6:110013000-110027400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:110013000-110027400	Weak transcription	Spleen	Spleen
8	chr6:110013000-110057000	Weak transcription	Left Ventricle	heart
9	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
10	chr6:110013200-110020200	Weak transcription	Colonic Mucosa	Colon
11	chr6:110013200-110022200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:110013200-110022400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:110013200-110024200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:110013200-110026400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr6:110013200-110026600	Weak transcription	Ovary	ovary
16	chr6:110013200-110034000	Weak transcription	Fetal Stomach	stomach
17	chr6:110013200-110057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:110013200-110057000	Weak transcription	Aorta	Aorta
19	chr6:110013400-110022200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:110013400-110023200	Weak transcription	Fetal Intestine Large	intestine
21	chr6:110013400-110038600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:110013600-110016600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:110013600-110017200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:110013600-110017200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:110013600-110018600	Weak transcription	Osteobl	bone
26	chr6:110013600-110022200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:110013600-110022400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:110013600-110022600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr6:110013600-110056000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr6:110013600-110056800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr6:110013800-110016600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:110013800-110018000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:110013800-110018600	Weak transcription	NHDF-Ad	bronchial
34	chr6:110013800-110026400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:110013800-110026600	Weak transcription	Brain Substantia Nigra	brain
36	chr6:110013800-110029600	Weak transcription	Fetal Lung	lung
37	chr6:110014000-110017600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:110014000-110027400	Weak transcription	Brain Angular Gyrus	brain
39	chr6:110014000-110034400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:110014200-110017200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:110014200-110017400	Weak transcription	Fetal Brain Male	brain
42	chr6:110014200-110018000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:110014400-110018600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:110014400-110023600	Weak transcription	Thymus	Thymus
45	chr6:110014600-110017800	Weak transcription	Brain Germinal Matrix	brain
46	chr6:110014600-110018000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:110014600-110018600	Weak transcription	Adipose Nuclei	Adipose
48	chr6:110014600-110022400	Weak transcription	Psoas Muscle	Psoas
49	chr6:110014600-110026600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:110014800-110018800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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