Variant report

Variant	rs9450704
Chromosome Location	chr6:88182704-88182705
allele	C/G
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	MAX	chr6:88182438-88182976	K562	blood:	n/a	chr6:88182680-88182690
2	CTCF	chr6:88182560-88182710	HPAF	blood vessel:	n/a	n/a
3	POLR2A	chr6:88182266-88183546	GM12891	blood:	n/a	n/a
4	TBP	chr6:88182152-88183512	GM12878	blood:	n/a	n/a
5	NFATC1	chr6:88182266-88182957	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:88182359-88183543	Hela-S3	cervix:	n/a	n/a
7	MAX	chr6:88182198-88183179	SK-N-SH	brain:	n/a	chr6:88182680-88182690
8	POLR2A	chr6:88182179-88183375	K562	blood:	n/a	n/a
9	MAX	chr6:88182310-88183391	GM12878	blood:	n/a	chr6:88182680-88182690
10	SPI1	chr6:88182598-88183034	GM12891	blood:	n/a	n/a
11	MAX	chr6:88182080-88183653	ECC-1	luminal epithelium:	n/a	chr6:88182680-88182690
12	TAF1	chr6:88182317-88183346	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:88182188-88183182	HEK293	kidney:	n/a	n/a
14	POLR2A	chr6:88182172-88183287	U87	brain:	n/a	n/a
15	POLR2A	chr6:88182286-88183338	MCF-7	breast:	n/a	n/a
16	CTCF	chr6:88182600-88182750	GM12878	blood:	n/a	n/a
17	UBTF	chr6:88182228-88183601	K562	blood:	n/a	n/a
18	TCF12	chr6:88182422-88183063	GM12878	blood:	n/a	n/a
19	KAP1	chr6:88182220-88183592	HEK293	kidney:	n/a	n/a
20	TAF1	chr6:88182274-88183231	A549	lung:	n/a	n/a
21	TCF3	chr6:88182466-88183146	GM12878	blood:	n/a	n/a
22	SIN3AK20	chr6:88182075-88183184	MCF-7	breast:	n/a	n/a
23	MAZ	chr6:88182213-88184221	IMR90	lung:	n/a	chr6:88182680-88182690
24	YY1	chr6:88182628-88182778	K562	blood:	n/a	chr6:88182677-88182691
25	POLR2A	chr6:88182345-88183068	GM10847	blood:	n/a	n/a
26	EP300	chr6:88182321-88183384	GM12878	blood:	n/a	chr6:88182664-88182680 chr6:88183173-88183189
27	ETS1	chr6:88182234-88182739	A549	lung:	n/a	chr6:88182390-88182403
28	POLR2A	chr6:88182187-88183545	HepG2	liver:	n/a	n/a
29	ELF1	chr6:88182157-88182949	SK-N-SH	brain:	n/a	chr6:88182677-88182689
30	POLR2A	chr6:88182231-88183456	GM12892	blood:	n/a	n/a
31	POLR2A	chr6:88182177-88183385	K562	blood:	n/a	n/a
32	YY1	chr6:88182497-88182812	HCT-116	colon:	n/a	chr6:88182677-88182691
33	IRF4	chr6:88182283-88182841	GM12878	blood:	n/a	n/a
34	ELF1	chr6:88182263-88183315	GM12878	blood:	n/a	chr6:88182677-88182689
35	POLR2A	chr6:88182088-88183148	SK-N-SH	brain:	n/a	n/a
36	TAF1	chr6:88182373-88182848	GM12891	blood:	n/a	n/a
37	POLR2A	chr6:88182359-88183164	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:88182195-88183596	HCT-116	colon:	n/a	n/a
39	TCF7L2	chr6:88182267-88183535	HCT-116	colon:	n/a	n/a
40	POLR2A	chr6:88182372-88183230	GM12891	blood:	n/a	n/a
41	POLR2A	chr6:88182576-88183131	H1-hESC	embryonic stem cell:	n/a	n/a
42	GABPA	chr6:88182133-88182952	HL-60	blood:	n/a	chr6:88182671-88182680
43	HEY1	chr6:88182216-88183216	K562	blood:	n/a	n/a
44	GTF2B	chr6:88182231-88183183	K562	blood:	n/a	n/a
45	ZNF263	chr6:88182216-88183695	HEK293-T-REx	kidney:	n/a	n/a
46	RELA	chr6:88182121-88183285	GM15510	blood:	n/a	n/a
47	MXI1	chr6:88181858-88184070	SK-N-SH	brain:	n/a	n/a
48	RCOR1	chr6:88182122-88183332	K562	blood:	n/a	n/a
49	SP2	chr6:88182188-88182893	HepG2	liver:	n/a	chr6:88182645-88182654
50	MAX	chr6:88182061-88183532	A549	lung:	n/a	chr6:88182680-88182690

No.	Distal block	Cell Line	Cell type
1	chr6:88180469..88184304-chr6:88409511..88413377,7	K562	blood:
2	chr1:45186914..45187800-chr6:88182273..88182944,2	HCT-116	colon:
3	chr6:88181828..88184241-chr6:88195546..88199503,4	MCF-7	breast:
4	chr6:88181757..88184109-chr6:88228159..88230300,2	MCF-7	breast:
5	chr6:88116849..88119599-chr6:88181543..88183591,3	MCF-7	breast:
6	chr6:87863665..87867000-chr6:88180798..88183159,3	K562	blood:
7	chr6:88181710..88183852-chr6:88298759..88301128,2	K562	blood:
8	chr6:88180469..88184304-chr6:88409409..88413377,5	K562	blood:

Variant related genes	Relation type
SLC35A1	TF binding region
ENSG00000146282	Chromatin interaction
ENSG00000188994	Chromatin interaction
ENSG00000272008	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000272514	Chromatin interaction
ENSG00000206715	Chromatin interaction
ENSG00000213204	Chromatin interaction
ENSG00000135336	Chromatin interaction
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1051131	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1051148	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10755484	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs13214153	0.96[CHB][hapmap];0.86[ASN][1000 genomes]
rs2103764	0.87[ASN][1000 genomes]
rs2207144	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs2207146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2268993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2268994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2273129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284908	1.00[CEU][hapmap];0.96[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2300906	1.00[CEU][hapmap];0.96[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2300909	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2325064	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3757368	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3918467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3934838	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs4334949	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4464759	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4587138	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4587143	1.00[CEU][hapmap];0.96[CHB][hapmap];0.92[JPT][hapmap]
rs4707374	0.81[EUR][1000 genomes]
rs6454630	0.86[CHB][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6454631	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6454632	0.84[EUR][1000 genomes]
rs6905947	0.96[CHB][hapmap];0.87[ASN][1000 genomes]
rs6906769	0.84[EUR][1000 genomes]
rs6912958	0.82[ASN][1000 genomes]
rs6914299	0.96[CHB][hapmap];0.86[ASN][1000 genomes]
rs6916732	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs6923230	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6933587	0.96[CHB][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7741825	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs7754350	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7757636	0.81[EUR][1000 genomes]
rs7761814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7762864	0.84[EUR][1000 genomes]
rs7773906	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs9294379	0.96[CHB][hapmap];0.86[ASN][1000 genomes]
rs9294381	0.96[CHB][hapmap];0.86[ASN][1000 genomes]
rs9444504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444512	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9444519	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs9444522	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs9450688	0.87[ASN][1000 genomes]
rs9450701	0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450712	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9450723	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9450732	1.00[CEU][hapmap];0.96[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes]
rs9450733	0.83[EUR][1000 genomes]
rs9450752	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs985764	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	21 gene(s)	inside rSNPs	diseases
6	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9450704	C6orf166	Cis_1M	lymphoblastoid	RTeQTL
rs9450704	ENSG00000164414	cis	multi-tissue	Pritchard
rs9450704	SLC35A1	cis	multi-tissue	Pritchard
rs9450704	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs9450704	C6orf162	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88181600-88183400	Active TSS	K562	blood
2	chr6:88181800-88183200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:88181800-88183200	Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr6:88181800-88183400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:88181800-88183400	Active TSS	Brain Cingulate Gyrus	brain
6	chr6:88181800-88183400	Active TSS	Brain Hippocampus Middle	brain
7	chr6:88181800-88183600	Active TSS	A549	lung
8	chr6:88181800-88183800	Active TSS	Psoas Muscle	Psoas
9	chr6:88182000-88182800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:88182000-88183200	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr6:88182000-88183200	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr6:88182000-88183200	Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr6:88182000-88183200	Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr6:88182000-88183200	Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr6:88182000-88183200	Active TSS	Liver	Liver
16	chr6:88182000-88183200	Active TSS	Brain Anterior Caudate	brain
17	chr6:88182000-88183200	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr6:88182000-88183200	Active TSS	Brain Substantia Nigra	brain
19	chr6:88182000-88183200	Active TSS	Colonic Mucosa	Colon
20	chr6:88182000-88183200	Active TSS	Duodenum Mucosa	Duodenum
21	chr6:88182000-88183200	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr6:88182000-88183200	Active TSS	Fetal Brain Female	brain
23	chr6:88182000-88183200	Active TSS	Fetal Muscle Leg	muscle
24	chr6:88182000-88183200	Active TSS	Fetal Thymus	thymus
25	chr6:88182000-88183200	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr6:88182000-88183200	Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr6:88182000-88183200	Active TSS	Thymus	Thymus
28	chr6:88182000-88183200	Active TSS	NH-A	brain
29	chr6:88182000-88183400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:88182000-88183400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:88182000-88183400	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr6:88182000-88183400	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr6:88182000-88183400	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr6:88182000-88183400	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr6:88182000-88183400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:88182000-88183400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr6:88182000-88183400	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr6:88182000-88183400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:88182000-88183400	Active TSS	Brain Angular Gyrus	brain
40	chr6:88182000-88183400	Active TSS	Colon Smooth Muscle	Colon
41	chr6:88182000-88183400	Active TSS	Fetal Heart	heart
42	chr6:88182000-88183400	Active TSS	Fetal Intestine Small	intestine
43	chr6:88182000-88183400	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr6:88182000-88183400	Active TSS	Fetal Lung	lung
45	chr6:88182000-88183400	Active TSS	Fetal Stomach	stomach
46	chr6:88182000-88183400	Active TSS	Pancreas	Pancrea
47	chr6:88182000-88183400	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr6:88182000-88183400	Active TSS	Rectal Smooth Muscle	rectum
49	chr6:88182000-88183400	Active TSS	Right Ventricle	heart
50	chr6:88182000-88183400	Active TSS	Stomach Smooth Muscle	stomach

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