Variant report

Variant	rs6568592
Chromosome Location	chr6:110000639-110000640
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
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	0.97[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	0.89[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[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	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12192776	0.90[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	0.90[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]
rs12197838	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197950	0.90[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	0.89[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	0.89[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	0.99[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	0.80[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	0.86[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	0.80[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	0.86[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	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3799845	0.86[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	0.93[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]
rs6906216	0.81[ASN][1000 genomes]
rs6911700	0.99[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	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs729888	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7341297	0.99[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	0.90[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: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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6568592	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs6568592	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs6568592	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs6568592	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs6568592	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109961400-110000800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:109978000-110010600	Weak transcription	Brain Germinal Matrix	brain
3	chr6:109980600-110011200	Weak transcription	Fetal Thymus	thymus
4	chr6:109983600-110000800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:109985200-110000800	Weak transcription	Spleen	Spleen
6	chr6:109989400-110011400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr6:109990000-110010600	Weak transcription	Fetal Intestine Small	intestine
8	chr6:109991400-110007200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:109991400-110010600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:109992000-110011200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:109992400-110011400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:109994400-110001000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:109998400-110010800	Weak transcription	Primary B cells from cord blood	blood
14	chr6:109999600-110000800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr6:109999600-110000800	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr6:109999600-110000800	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr6:109999800-110000800	Active TSS	Pancreas	Pancrea
18	chr6:109999800-110001000	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr6:110000000-110000800	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr6:110000000-110001000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:110000200-110000800	Enhancers	Placenta	Placenta
22	chr6:110000200-110001000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:110000200-110001000	Active TSS	HepG2	liver
24	chr6:110000400-110001000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr6:110000400-110011400	Weak transcription	Left Ventricle	heart
26	chr6:110000600-110000800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr6:110000600-110000800	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr6:110000600-110001000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr6:110000600-110001000	Enhancers	H9 Cell Line	embryonic stem cell
30	chr6:110000600-110001000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:110000600-110001000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr6:110000600-110001000	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr6:110000600-110001000	Enhancers	Lung	lung
34	chr6:110000600-110001000	Enhancers	Thymus	Thymus
35	chr6:110000600-110001200	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr6:110000600-110010800	Weak transcription	Stomach Smooth Muscle	stomach

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