Variant report

Variant	rs6454634
Chromosome Location	chr6:88300626-88300627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr6:88300605-88300899	K562	blood:	n/a	n/a
2	TBP	chr6:88300598-88300869	K562	blood:	n/a	n/a
3	POLR2A	chr6:88299102-88300725	HepG2	liver:	n/a	n/a
4	MAX	chr6:88300509-88301022	K562	blood:	n/a	n/a
5	E2F4	chr6:88299204-88300993	MCF10A-Er-Src	breast:	n/a	chr6:88299841-88299848 chr6:88299841-88299848 chr6:88299838-88299849 chr6:88299837-88299849 chr6:88299781-88299790 chr6:88299841-88299848
6	MXI1	chr6:88300493-88300859	K562	blood:	n/a	n/a
7	POLR2A	chr6:88300561-88301066	PANC-1	pancreas:	n/a	n/a
8	MYC	chr6:88300610-88300943	K562	blood:	n/a	n/a
9	REST	chr6:88300570-88301163	HL-60	blood:	n/a	n/a
10	MXI1	chr6:88298424-88301082	SK-N-SH	brain:	n/a	n/a
11	FOS	chr6:88300579-88300833	MCF10A-Er-Src	breast:	n/a	n/a
12	MAZ	chr6:88300437-88300783	K562	blood:	n/a	n/a
13	MYC	chr6:88300509-88301008	K562	blood:	n/a	n/a
14	POLR2A	chr6:88299308-88300814	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr6:88298955-88300882	GM12891	blood:	n/a	n/a
16	MXI1	chr6:88298616-88301102	IMR90	lung:	n/a	n/a
17	MYC	chr6:88299173-88301025	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:88300543..88303265-chr6:88372945..88374900,2	K562	blood:
2	chr6:88298942..88303064-chr6:88409165..88412231,4	K562	blood:
3	chr6:88299673..88301546-chr6:89673147..89674942,2	K562	blood:
4	chr6:88299988..88301682-chr6:88305873..88308812,2	K562	blood:
5	chr6:88300267..88302133-chr6:88313231..88315132,2	MCF-7	breast:
6	chr6:88300436..88304356-chr6:88305861..88309850,4	MCF-7	breast:
7	chr6:88300479..88302167-chr6:88410485..88412465,2	MCF-7	breast:
8	chr6:88299553..88301559-chr6:88410382..88412634,2	MCF-7	breast:
9	chr6:88181710..88183852-chr6:88298759..88301128,2	K562	blood:
10	chr6:88299715..88302499-chr6:88315597..88317409,2	MCF-7	breast:
11	chr6:88277452..88280023-chr6:88298199..88301235,3	MCF-7	breast:

No data

Variant related genes	Relation type
RARS2	TF binding region
ENSG00000135334	Chromatin interaction
ENSG00000111880	Chromatin interaction
ENSG00000146282	Chromatin interaction
ENSG00000135336	Chromatin interaction
ENSG00000164414	Chromatin interaction
ENSG00000203863	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1052623	0.94[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs1075665	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11962148	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11965562	0.90[CHB][hapmap]
rs11970493	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11970696	0.91[CHB][hapmap]
rs12524205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12529993	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12530371	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13214442	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs16879887	0.85[CHB][hapmap]
rs16879893	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2223877	0.90[CHB][hapmap]
rs2246051	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2246057	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2268996	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2295088	0.95[CHB][hapmap]
rs2300898	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2300899	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2300900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2300904	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs2300908	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs34513746	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3778671	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs3818057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4132446	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4354121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707378	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4707385	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs58305152	0.91[ASN][1000 genomes]
rs6914244	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915077	0.91[CHB][hapmap]
rs6927171	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs6928057	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs728582	0.90[CHB][hapmap]
rs7649	1.00[CHB][hapmap]
rs7759462	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7761943	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs9294384	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9294385	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9444499	0.91[CHB][hapmap]
rs9444501	0.91[CHB][hapmap]
rs9444509	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs9444511	0.80[ASN][1000 genomes]
rs9444513	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9444514	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9444516	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444521	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444531	0.85[EUR][1000 genomes]
rs9444534	0.81[EUR][1000 genomes]
rs9450677	0.89[CHB][hapmap]
rs9450681	0.90[CHB][hapmap]
rs9450686	0.90[CHB][hapmap]
rs9450693	0.91[CHB][hapmap]
rs9450694	0.84[CHB][hapmap]
rs9450697	0.90[CHB][hapmap]
rs9450698	0.90[CHB][hapmap]
rs9450699	1.00[CHB][hapmap]
rs9450700	1.00[CHB][hapmap]
rs9450708	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs9450709	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs9450716	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9450717	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9450728	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9450729	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9450734	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450735	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450740	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9450741	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450743	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450749	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450760	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450763	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9474	0.94[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][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	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
2	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
3	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
4	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
5	nsv538354	chr6:88273858-88311606	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6454634	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs6454634	SLC35A1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88297800-88301200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:88297800-88301400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr6:88298000-88300800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:88298000-88301000	Active TSS	HSMM	muscle
5	chr6:88298000-88301400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:88298000-88301400	Active TSS	A549	lung
7	chr6:88298200-88300800	Active TSS	Fetal Intestine Large	intestine
8	chr6:88298200-88301000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:88298200-88301000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:88298200-88301200	Active TSS	H1 Cell Line	embryonic stem cell
11	chr6:88298400-88300800	Active TSS	Fetal Muscle Trunk	muscle
12	chr6:88298400-88300800	Active TSS	Right Atrium	heart
13	chr6:88298400-88300800	Active TSS	HSMMtube	muscle
14	chr6:88298400-88301000	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr6:88298600-88300800	Active TSS	Aorta	Aorta
16	chr6:88298600-88300800	Active TSS	Left Ventricle	heart
17	chr6:88298600-88300800	Active TSS	Psoas Muscle	Psoas
18	chr6:88298600-88301000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr6:88298600-88301000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:88298800-88300800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:88298800-88300800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:88298800-88300800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:88298800-88300800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:88298800-88300800	Active TSS	GM12878-XiMat	blood
25	chr6:88298800-88301000	Active TSS	H9 Cell Line	embryonic stem cell
26	chr6:88298800-88301200	Active TSS	NHDF-Ad	bronchial
27	chr6:88298800-88301400	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr6:88299000-88300800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:88299000-88300800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:88299000-88300800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:88299000-88300800	Active TSS	Brain Germinal Matrix	brain
32	chr6:88299000-88301000	Active TSS	Brain Angular Gyrus	brain
33	chr6:88299000-88301400	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr6:88299200-88300800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:88299200-88300800	Active TSS	Placenta	Placenta
36	chr6:88299200-88300800	Active TSS	Fetal Thymus	thymus
37	chr6:88299200-88301000	Active TSS	Right Ventricle	heart
38	chr6:88299200-88301200	Active TSS	Hela-S3	cervix
39	chr6:88300000-88300800	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr6:88300000-88300800	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr6:88300000-88301000	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr6:88300000-88301200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:88300200-88300800	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr6:88300200-88300800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:88300200-88301000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr6:88300200-88301000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr6:88300200-88301000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:88300200-88301000	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr6:88300200-88301000	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr6:88300200-88301000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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