Variant report

Variant	rs12192268
Chromosome Location	chr6:110011458-110011459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr6:110011376-110013013	IMR90	lung:	n/a	n/a
2	POLR2A	chr6:110011312-110012900	H1-hESC	embryonic stem cell:	n/a	n/a
3	SIN3A	chr6:110011432-110013084	H1-hESC	embryonic stem cell:	n/a	chr6:110012719-110012730
4	NRF1	chr6:110011369-110012986	SK-N-SH	brain:	n/a	chr6:110011916-110011927 chr6:110012260-110012267
5	REST	chr6:110011287-110013024	H1-neurons	neurons:	n/a	chr6:110012894-110012903 chr6:110012991-110013011
6	TAF1	chr6:110011449-110012933	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
FIG4	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10457192	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs10457194	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes]
rs10457195	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs10457203	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10499053	0.85[CHB][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap]
rs10782163	0.83[EUR][1000 genomes]
rs11153183	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs11153188	0.85[EUR][1000 genomes]
rs11153213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11153214	0.92[ASN][1000 genomes]
rs11153215	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11153216	0.83[AMR][1000 genomes]
rs11752791	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11754340	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11754455	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes]
rs11755641	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11968978	0.87[MKK][hapmap]
rs12190372	0.81[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes]
rs12191353	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12192776	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12193719	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12194061	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs12194157	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12197180	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes]
rs12197838	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12197950	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12198938	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs12199154	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs12201356	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12201444	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12203993	0.83[AMR][1000 genomes]
rs12204548	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12205140	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12205485	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12208018	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12208933	0.90[CHB][hapmap]
rs12210706	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12212476	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs12214639	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12215077	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12528392	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes]
rs12528781	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13191066	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13198852	0.83[AMR][1000 genomes]
rs13199109	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13199135	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13201430	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs13201947	0.83[EUR][1000 genomes]
rs13201951	0.85[EUR][1000 genomes]
rs13203587	0.81[EUR][1000 genomes]
rs1321328	0.90[CHB][hapmap]
rs13220915	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs1322124	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1406899	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes]
rs1476388	0.81[EUR][1000 genomes]
rs1960325	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1980591	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2024849	0.81[EUR][1000 genomes]
rs2024850	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2024852	0.81[EUR][1000 genomes]
rs2024853	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs2025147	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes]
rs2025148	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2273752	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2277114	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2357124	0.84[EUR][1000 genomes]
rs36131450	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3799845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799849	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3899233	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4141930	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4490694	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4945833	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4947016	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6568592	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6911700	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6914498	0.90[CHB][hapmap]
rs71541003	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs729888	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7341297	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7451512	0.83[AMR][1000 genomes]
rs749517	0.83[EUR][1000 genomes]
rs7755941	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs7767525	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7773950	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs971434	0.90[CHB][hapmap];0.86[YRI][hapmap]

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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12192268	AKD1	cis	parietal	SCAN
rs12192268	FIG4	cis	cerebellum	SCAN
rs12192268	PDSS2	cis	cerebellum	SCAN
rs12192268	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs12192268	SMPD2	cis	Whole Blood	GTEx
rs12192268	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs12192268	CD164	cis	parietal	SCAN
rs12192268	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs12192268	AKD1	cis	cerebellum	SCAN
rs12192268	SMPD2	cis	parietal	SCAN
rs12192268	FIG4	cis	parietal	SCAN
rs12192268	AKD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110001200-110011600	Weak transcription	Spleen	Spleen
2	chr6:110010800-110013600	Active TSS	Stomach Smooth Muscle	stomach
3	chr6:110011000-110011600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:110011000-110011600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr6:110011000-110011600	Weak transcription	Esophagus	oesophagus
6	chr6:110011000-110011800	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr6:110011000-110011800	Flanking Active TSS	Dnd41	blood
8	chr6:110011000-110012200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:110011000-110013000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:110011000-110013400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr6:110011000-110013600	Active TSS	H1 Cell Line	embryonic stem cell
12	chr6:110011000-110013600	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:110011000-110013600	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr6:110011000-110013800	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr6:110011200-110011600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr6:110011200-110011600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr6:110011200-110011600	Flanking Active TSS	HepG2	liver
18	chr6:110011200-110012000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr6:110011200-110012000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:110011200-110012000	Active TSS	Brain Germinal Matrix	brain
21	chr6:110011200-110012200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:110011200-110012800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:110011200-110012800	Active TSS	Duodenum Mucosa	Duodenum
24	chr6:110011200-110013000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:110011200-110013000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:110011200-110013000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr6:110011200-110013000	Active TSS	Brain Anterior Caudate	brain
28	chr6:110011200-110013000	Active TSS	Colon Smooth Muscle	Colon
29	chr6:110011200-110013000	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr6:110011200-110013200	Active TSS	Brain Cingulate Gyrus	brain
31	chr6:110011200-110013200	Active TSS	Fetal Brain Male	brain
32	chr6:110011200-110013200	Active TSS	Fetal Intestine Small	intestine
33	chr6:110011200-110013200	Active TSS	Psoas Muscle	Psoas
34	chr6:110011200-110013400	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr6:110011200-110013400	Active TSS	NHLF	lung
36	chr6:110011200-110013600	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr6:110011200-110013600	Active TSS	Fetal Kidney	kidney
38	chr6:110011200-110015000	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr6:110011400-110011600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
40	chr6:110011400-110011600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:110011400-110011600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:110011400-110011600	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr6:110011400-110011600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:110011400-110011600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr6:110011400-110011600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr6:110011400-110011600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr6:110011400-110011600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr6:110011400-110011600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:110011400-110011600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:110011400-110011600	Active TSS	Fetal Muscle Trunk	muscle

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