Variant report

Variant	rs6454589
Chromosome Location	chr6:87861785-87861786
allele	G/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	NFIC	chr6:87861463-87862605	GM12878	blood:	n/a	n/a
2	MAX	chr6:87861623-87862245	MCF-7	breast:	n/a	chr6:87862031-87862041
3	POLR2A	chr6:87861210-87863425	GM12891	blood:	n/a	n/a
4	POLR2A	chr6:87861315-87861935	U87	brain:	n/a	n/a
5	POLR2A	chr6:87861390-87862355	GM12878	blood:	n/a	n/a
6	TCF3	chr6:87861664-87862106	GM12878	blood:	n/a	n/a
7	PAX5	chr6:87861665-87862190	GM12878	blood:	n/a	chr6:87861862-87861881
8	POLR2A	chr6:87861574-87862124	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr6:87861650-87862207	GM12878	blood:	n/a	n/a
10	TAF1	chr6:87861209-87862480	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr6:87861353-87862415	GM12892	blood:	n/a	n/a
12	MAX	chr6:87861197-87862462	GM12878	blood:	n/a	chr6:87862031-87862041
13	GTF2F1	chr6:87861341-87862299	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr6:87861302-87862300	Gliobla	brain:	n/a	n/a
15	YY1	chr6:87861325-87862299	GM12892	blood:	n/a	chr6:87861581-87861595 chr6:87862114-87862128 chr6:87862037-87862048
16	REST	chr6:87861087-87862586	H1-neurons	neurons:	n/a	chr6:87861585-87861595
17	STAT5A	chr6:87861611-87862742	GM12878	blood:	n/a	n/a
18	TAF1	chr6:87861364-87862332	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr6:87861328-87862606	SK-N-SH	brain:	n/a	chr6:87862031-87862041
20	POLR2A	chr6:87861324-87862560	PANC-1	pancreas:	n/a	n/a
21	RCOR1	chr6:87861168-87862574	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:87861348-87862623	GM12878	blood:	n/a	n/a
23	YY1	chr6:87861300-87862390	SK-N-SH_RA	brain:	n/a	chr6:87861581-87861595 chr6:87862114-87862128 chr6:87862037-87862048
24	POLR2A	chr6:87861481-87862352	H1-neurons	neurons:	n/a	n/a
25	TAF1	chr6:87861249-87862406	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr6:87861660-87861810	GM12872	blood:	n/a	n/a
27	POLR2A	chr6:87861388-87862314	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAZ	chr6:87861328-87862672	GM12878	blood:	n/a	chr6:87862031-87862041
29	NFIC	chr6:87861297-87861949	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr6:87861456-87862230	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr6:87861161-87862704	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:87861114-87862547	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr6:87861645-87862349	MCF-7	breast:	n/a	n/a
34	YY1	chr6:87861343-87862160	H1-hESC	embryonic stem cell:	n/a	chr6:87861581-87861595 chr6:87862114-87862128 chr6:87862037-87862048
35	POLR2A	chr6:87861634-87862475	GM12892	blood:	n/a	n/a
36	USF1	chr6:87861521-87861940	ECC-1	luminal epithelium:	n/a	chr6:87861585-87861601
37	NFIC	chr6:87861251-87861969	ECC-1	luminal epithelium:	n/a	n/a
38	YY1	chr6:87861633-87862181	GM12891	blood:	n/a	chr6:87862114-87862128 chr6:87862037-87862048
39	ZBTB7A	chr6:87861198-87861838	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr6:87861516-87862360	GM12891	blood:	n/a	n/a
41	POU2F2	chr6:87861547-87862101	GM12891	blood:	n/a	n/a
42	POLR2A	chr6:87861233-87862702	SK-N-MC	brain:	n/a	n/a
43	POLR2A	chr6:87861264-87862945	GM19099	blood:	n/a	n/a
44	BHLHE40	chr6:87861139-87862710	GM12878	blood:	n/a	chr6:87861585-87861601
45	POLR2A	chr6:87861433-87862398	IMR90	lung:	n/a	n/a
46	MYC	chr6:87861662-87862197	MCF-7	breast:	n/a	chr6:87862031-87862041
47	BCLAF1	chr6:87861428-87862334	GM12878	blood:	n/a	chr6:87861592-87861601 chr6:87861960-87861968 chr6:87862035-87862048 chr6:87861583-87861596
48	MAX	chr6:87861258-87862231	ECC-1	luminal epithelium:	n/a	chr6:87862031-87862041
49	POLR2A	chr6:87861216-87862359	PANC-1	pancreas:	n/a	n/a
50	MAX	chr6:87861418-87862531	SK-N-SH	brain:	n/a	chr6:87862031-87862041

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:87860967..87863617-chr6:87863794..87865835,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CGA-2	chr6:87860877-87865003	ENSG00000272008.1

Variant related genes	Relation type
ZNF292	TF binding region
ENSG00000272008	Chromatin interaction
ENSG00000188994	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1080595	0.83[ASN][1000 genomes]
rs1080596	0.83[ASN][1000 genomes]
rs12176253	0.86[EUR][1000 genomes]
rs12664578	0.83[ASN][1000 genomes]
rs1813847	0.85[ASN][1000 genomes]
rs1813848	0.85[ASN][1000 genomes]
rs1886751	0.87[ASN][1000 genomes]
rs1886752	0.87[ASN][1000 genomes]
rs1925688	0.85[ASN][1000 genomes]
rs1925689	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1925695	0.81[ASN][1000 genomes]
rs1980790	0.83[ASN][1000 genomes]
rs1980791	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1980792	0.83[ASN][1000 genomes]
rs1998765	0.83[ASN][1000 genomes]
rs2025630	0.86[ASN][1000 genomes]
rs2031518	0.83[ASN][1000 genomes]
rs2031519	0.83[ASN][1000 genomes]
rs2147917	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2147918	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2147919	0.81[ASN][1000 genomes]
rs2147920	0.81[ASN][1000 genomes]
rs2147921	0.81[ASN][1000 genomes]
rs2182181	0.81[ASN][1000 genomes]
rs2240460	0.82[EUR][1000 genomes]
rs35788380	0.85[EUR][1000 genomes]
rs3734187	0.86[EUR][1000 genomes]
rs3812130	0.86[EUR][1000 genomes]
rs3846773	0.88[EUR][1000 genomes]
rs3846774	0.88[EUR][1000 genomes]
rs3846775	0.88[EUR][1000 genomes]
rs3846776	0.88[EUR][1000 genomes]
rs3857483	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3857484	0.90[EUR][1000 genomes]
rs4099964	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4269346	0.85[ASN][1000 genomes]
rs4489129	0.85[ASN][1000 genomes]
rs4533962	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4540237	0.85[ASN][1000 genomes]
rs4574603	0.86[EUR][1000 genomes]
rs4591818	0.88[EUR][1000 genomes]
rs4706289	0.83[ASN][1000 genomes]
rs4707346	0.81[ASN][1000 genomes]
rs4707347	0.80[ASN][1000 genomes]
rs4707348	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4707357	0.86[EUR][1000 genomes]
rs62439492	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6454584	0.85[ASN][1000 genomes]
rs6454587	0.85[ASN][1000 genomes]
rs6454588	0.85[ASN][1000 genomes]
rs6454591	0.83[ASN][1000 genomes]
rs6454592	0.82[ASN][1000 genomes]
rs6454593	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6454596	0.85[EUR][1000 genomes]
rs6454597	0.85[EUR][1000 genomes]
rs6454599	0.86[EUR][1000 genomes]
rs6899394	0.86[EUR][1000 genomes]
rs6904310	0.83[ASN][1000 genomes]
rs6907805	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6909021	0.85[ASN][1000 genomes]
rs6909200	0.83[ASN][1000 genomes]
rs6910991	0.88[EUR][1000 genomes]
rs6913932	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6914193	0.80[ASN][1000 genomes]
rs6916994	0.85[EUR][1000 genomes]
rs6921007	0.86[EUR][1000 genomes]
rs6921619	0.86[ASN][1000 genomes]
rs6926563	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6926838	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6927748	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6929920	0.83[ASN][1000 genomes]
rs6932678	0.86[EUR][1000 genomes]
rs6933046	0.90[EUR][1000 genomes]
rs6934603	0.86[EUR][1000 genomes]
rs6934717	0.83[ASN][1000 genomes]
rs6937874	0.86[EUR][1000 genomes]
rs6940544	0.85[EUR][1000 genomes]
rs7453986	0.86[EUR][1000 genomes]
rs7739034	0.83[ASN][1000 genomes]
rs7739726	0.83[ASN][1000 genomes]
rs7742478	0.83[ASN][1000 genomes]
rs7742710	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7748191	0.83[ASN][1000 genomes]
rs7748879	0.81[ASN][1000 genomes]
rs7751029	0.82[ASN][1000 genomes]
rs7752485	0.80[ASN][1000 genomes]
rs7753030	0.86[EUR][1000 genomes]
rs7755883	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7757199	0.85[ASN][1000 genomes]
rs7757827	0.81[ASN][1000 genomes]
rs7763365	0.83[ASN][1000 genomes]
rs7766324	0.83[ASN][1000 genomes]
rs7767449	0.83[ASN][1000 genomes]
rs7768575	0.83[ASN][1000 genomes]
rs7774080	0.87[EUR][1000 genomes]
rs7774603	0.90[EUR][1000 genomes]
rs7776407	0.83[ASN][1000 genomes]
rs9294367	0.85[ASN][1000 genomes]
rs9294370	0.84[ASN][1000 genomes]
rs9294371	0.81[ASN][1000 genomes]
rs9294372	0.87[ASN][1000 genomes]
rs9294374	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9344677	0.81[ASN][1000 genomes]
rs9344690	0.81[ASN][1000 genomes]
rs9344691	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9344695	0.88[EUR][1000 genomes]
rs9344696	0.87[EUR][1000 genomes]
rs9351114	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9351117	0.85[ASN][1000 genomes]
rs9353455	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9353456	0.83[ASN][1000 genomes]
rs9353462	0.86[ASN][1000 genomes]
rs9353463	0.83[ASN][1000 genomes]
rs9353466	0.81[EUR][1000 genomes]
rs9353468	0.86[EUR][1000 genomes]
rs9353473	0.86[EUR][1000 genomes]
rs9359734	0.86[EUR][1000 genomes]
rs9359736	0.83[ASN][1000 genomes]
rs9359743	0.86[EUR][1000 genomes]
rs9362398	0.81[ASN][1000 genomes]
rs9362401	0.83[ASN][1000 genomes]
rs9362408	0.83[ASN][1000 genomes]
rs9362411	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9362413	0.90[EUR][1000 genomes]
rs9362415	0.86[EUR][1000 genomes]
rs9362417	0.86[EUR][1000 genomes]
rs9444479	0.87[ASN][1000 genomes]
rs9450634	0.81[ASN][1000 genomes]
rs9450647	0.86[EUR][1000 genomes]
rs9450650	0.86[EUR][1000 genomes]
rs9450652	0.85[EUR][1000 genomes]
rs994170	0.85[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	nsv1024751	chr6:87433199-87908721	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv604114	chr6:87816905-87906053	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv3366503	chr6:87849282-87862940	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6454589	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs6454589	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs6454589	C6orf162	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87860800-87862400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:87860800-87862800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr6:87861000-87861800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:87861000-87862200	Active TSS	Brain Hippocampus Middle	brain
5	chr6:87861000-87862400	Active TSS	Fetal Brain Female	brain
6	chr6:87861000-87863200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:87861000-87866200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:87861200-87861800	Active TSS	H1 Cell Line	embryonic stem cell
9	chr6:87861200-87861800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:87861200-87861800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:87861200-87861800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:87861200-87861800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:87861200-87861800	Active TSS	Esophagus	oesophagus
14	chr6:87861200-87861800	Enhancers	Fetal Heart	heart
15	chr6:87861200-87861800	Active TSS	Pancreas	Pancrea
16	chr6:87861200-87861800	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr6:87861200-87861800	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr6:87861200-87861800	Flanking Active TSS	NH-A	brain
19	chr6:87861200-87862000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:87861200-87862000	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr6:87861200-87862000	Enhancers	Fetal Brain Male	brain
22	chr6:87861200-87862000	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr6:87861200-87862200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:87861200-87862200	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr6:87861200-87862200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:87861200-87862200	Active TSS	Primary T cells from cord blood	blood
27	chr6:87861200-87862200	Active TSS	Colon Smooth Muscle	Colon
28	chr6:87861200-87862200	Active TSS	Duodenum Mucosa	Duodenum
29	chr6:87861200-87862200	Active TSS	Left Ventricle	heart
30	chr6:87861200-87862400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:87861200-87862400	Flanking Active TSS	Colonic Mucosa	Colon
32	chr6:87861200-87862400	Active TSS	Fetal Lung	lung
33	chr6:87861200-87862400	Active TSS	Fetal Stomach	stomach
34	chr6:87861200-87862600	Active TSS	H9 Cell Line	embryonic stem cell
35	chr6:87861200-87862600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:87861200-87862600	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr6:87861200-87862600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:87861200-87862600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr6:87861200-87862600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr6:87861200-87862600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr6:87861200-87862600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:87861200-87862600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:87861200-87862600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:87861200-87862600	Active TSS	Brain Germinal Matrix	brain
45	chr6:87861200-87862600	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr6:87861200-87862600	Active TSS	Fetal Kidney	kidney
47	chr6:87861200-87862600	Active TSS	Ovary	ovary
48	chr6:87861200-87862600	Active TSS	Right Ventricle	heart
49	chr6:87861200-87862600	Active TSS	HSMMtube	muscle
50	chr6:87861200-87862600	Flanking Active TSS	HUVEC	blood vessel

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