Variant report

Variant	rs12197838
Chromosome Location	chr6:109993291-109993292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10457192	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10457194	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10457195	0.86[EUR][1000 genomes]
rs10457203	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10499053	0.86[ASN][1000 genomes]
rs10782163	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11153183	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11153188	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11153213	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11153215	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11153216	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11752791	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11754340	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11754455	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11755641	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11758651	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12190372	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12191353	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12192268	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12192776	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12193719	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12194061	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12194157	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12197180	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12197950	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12198938	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12199154	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12201356	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12201444	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12203993	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12204548	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12205140	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12205485	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12208018	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12208933	0.84[ASN][1000 genomes]
rs12210706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212476	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12214639	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12215077	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12528392	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12528781	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13191066	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13198852	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13199109	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13199135	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13201430	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13201947	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13201951	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13203587	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13204102	0.83[ASN][1000 genomes]
rs13204500	0.88[ASN][1000 genomes]
rs1321328	0.91[ASN][1000 genomes]
rs13220915	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1322124	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1406899	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1476388	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1960325	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1980591	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1998811	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2024849	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2024850	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2024852	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2024853	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2025147	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2025148	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2208209	0.84[ASN][1000 genomes]
rs2273752	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2277114	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2357124	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36131450	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3799845	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3799849	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3899233	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4141930	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4490694	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4945833	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4947016	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6568592	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906216	0.81[ASN][1000 genomes]
rs6911700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6914498	0.84[ASN][1000 genomes]
rs6920292	0.83[ASN][1000 genomes]
rs6926096	0.81[ASN][1000 genomes]
rs71541003	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs729888	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7341297	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7451512	0.80[AMR][1000 genomes]
rs749517	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7755941	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7767525	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7773950	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs971434	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026012	chr6:109851638-109999379	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv604484	chr6:109851937-109997529	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12197838	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs12197838	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs12197838	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs12197838	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs12197838	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109948000-109995000	Weak transcription	Brain Anterior Caudate	brain
2	chr6:109954400-109994800	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:109961400-110000800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:109961600-110000600	Weak transcription	Thymus	Thymus
5	chr6:109965200-110000600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:109967800-109997000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:109978000-110010600	Weak transcription	Brain Germinal Matrix	brain
8	chr6:109979600-110000600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr6:109980200-109999800	Weak transcription	Pancreas	Pancrea
10	chr6:109980600-109998600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:109980600-110011200	Weak transcription	Fetal Thymus	thymus
12	chr6:109983600-110000800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:109985200-110000800	Weak transcription	Spleen	Spleen
14	chr6:109986800-109994600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:109987200-109998400	Weak transcription	Aorta	Aorta
16	chr6:109988200-109998600	Weak transcription	Fetal Heart	heart
17	chr6:109988600-109998000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:109989200-109995400	Weak transcription	Fetal Stomach	stomach
19	chr6:109989200-109998200	Weak transcription	Small Intestine	intestine
20	chr6:109989400-109997600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr6:109989400-110011400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr6:109989600-109994200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:109990000-110010600	Weak transcription	Fetal Intestine Small	intestine
24	chr6:109990800-109995000	Enhancers	HUVEC	blood vessel
25	chr6:109991000-109999600	Weak transcription	Primary T cells from cord blood	blood
26	chr6:109991200-109995000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:109991200-109995600	Weak transcription	Ovary	ovary
28	chr6:109991400-110007200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:109991400-110010600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:109992000-110011200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:109992200-109994600	Enhancers	NHDF-Ad	bronchial
32	chr6:109992400-109993600	Enhancers	Osteobl	bone
33	chr6:109992400-109993800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr6:109992400-109994600	Enhancers	NHLF	lung
35	chr6:109992400-110011400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:109992600-109993400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr6:109992600-109993600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:109992600-109993600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:109992600-109993600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:109992600-109993800	Strong transcription	Primary B cells from cord blood	blood
41	chr6:109992600-109994400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:109992800-109993400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:109992800-109994000	Strong transcription	Left Ventricle	heart
44	chr6:109993000-109993400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr6:109993000-109993800	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr6:109993000-109994800	Weak transcription	Liver	Liver
47	chr6:109993200-109993800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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