Variant report

Variant	rs2246051
Chromosome Location	chr6:88194020-88194021
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:68)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:68 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr6:88193686-88194025	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr6:88193636-88194175	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr6:88193880-88194030	HPAF	blood vessel:	n/a	n/a
4	RAD21	chr6:88193721-88194086	HepG2	liver:	n/a	n/a
5	CTCF	chr6:88193880-88194030	GM12865	blood:	n/a	n/a
6	RAD21	chr6:88193828-88194078	GM12878	blood:	n/a	n/a
7	SMC3	chr6:88193805-88194080	K562	blood:	n/a	n/a
8	RAD21	chr6:88193800-88194086	GM12878	blood:	n/a	n/a
9	CTCF	chr6:88193880-88194030	GM12872	blood:	n/a	n/a
10	CTCF	chr6:88193827-88194034	MCF-7	breast:	n/a	n/a
11	RAD21	chr6:88193857-88194081	SK-N-SH_RA	brain:	n/a	n/a
12	JUND	chr6:88193574-88194742	HCT-116	colon:	n/a	n/a
13	CTCF	chr6:88193880-88194030	HCT-116	colon:	n/a	n/a
14	CTCF	chr6:88193843-88194025	GM12892	blood:	n/a	n/a
15	ZNF143	chr6:88193850-88194039	K562	blood:	n/a	n/a
16	TEAD4	chr6:88193589-88194158	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr6:88194020-88194170	NHEK	skin:	n/a	n/a
18	CTCF	chr6:88193880-88194030	GM12875	blood:	n/a	n/a
19	RCOR1	chr6:88193863-88194048	K562	blood:	n/a	n/a
20	SMC3	chr6:88193881-88194031	GM12878	blood:	n/a	n/a
21	CTCF	chr6:88193900-88194050	SK-N-SH_RA	brain:	n/a	n/a
22	TAF1	chr6:88193640-88194063	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr6:88193784-88194040	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCFL	chr6:88193806-88194024	K562	blood:	n/a	n/a
25	CTCF	chr6:88193739-88194069	K562	blood:	n/a	n/a
26	CTCF	chr6:88193701-88194089	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr6:88193768-88194111	GM12878	blood:	n/a	n/a
28	CTCF	chr6:88193854-88194034	A549	lung:	n/a	n/a
29	CTCF	chr6:88193828-88194055	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr6:88193757-88194114	K562	blood:	n/a	n/a
31	JUND	chr6:88193610-88194102	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr6:88193470-88194103	HCT-116	colon:	n/a	n/a
33	CTCF	chr6:88193854-88194033	MCF-7	breast:	n/a	n/a
34	YY1	chr6:88193633-88194051	HCT-116	colon:	n/a	n/a
35	SMC3	chr6:88193815-88194038	HepG2	liver:	n/a	n/a
36	FOSL1	chr6:88193459-88194848	HCT-116	colon:	n/a	n/a
37	CTCF	chr6:88193880-88194030	HBMEC	blood vessel:	n/a	n/a
38	CTCF	chr6:88193702-88194228	K562	blood:	n/a	n/a
39	CTCF	chr6:88193745-88194081	HepG2	liver:	n/a	n/a
40	CTCF	chr6:88193837-88194066	Medullo	brain:	n/a	n/a
41	RAD21	chr6:88193740-88194128	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr6:88193880-88194030	HFF-Myc	foreskin:	n/a	n/a
43	ZNF143	chr6:88193648-88194099	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr6:88193830-88194050	GM12878	blood:	n/a	n/a
45	CTCF	chr6:88193880-88194030	GM12878	blood:	n/a	n/a
46	CTCF	chr6:88193847-88194024	HepG2	liver:	n/a	n/a
47	RAD21	chr6:88193891-88194096	HepG2	liver:	n/a	n/a
48	TEAD4	chr6:88193591-88194056	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr6:88193798-88194122	K562	blood:	n/a	n/a
50	SP1	chr6:88193381-88194873	HCT-116	colon:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:88181541..88186084-chr6:88193253..88197004,5	MCF-7	breast:
2	chr6:88187817..88189806-chr6:88192099..88194936,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNU6-444P	TF binding region
ENSG00000164414	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10944310	1.00[CHB][hapmap]
rs11962148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11965562	1.00[CHB][hapmap]
rs11970696	1.00[CHB][hapmap]
rs12524205	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs12530371	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs13214442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1328477	0.81[CHB][hapmap]
rs16879887	0.95[CHB][hapmap]
rs16879893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2223877	1.00[CHB][hapmap]
rs2246057	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2268996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap]
rs2295088	0.86[CHB][hapmap]
rs2300898	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2300899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap]
rs2300900	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2300904	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2300908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3778671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3818057	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs4354121	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs6454634	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs6915077	1.00[CHB][hapmap]
rs6927171	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6928057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs728582	1.00[CHB][hapmap]
rs7649	0.90[CHB][hapmap]
rs7761943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap]
rs9294385	0.84[JPT][hapmap]
rs9444499	1.00[CHB][hapmap]
rs9444501	1.00[CHB][hapmap]
rs9444509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9444514	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs9450659	0.95[CHB][hapmap]
rs9450667	1.00[CHB][hapmap]
rs9450677	1.00[CHB][hapmap]
rs9450681	1.00[CHB][hapmap]
rs9450686	1.00[CHB][hapmap]
rs9450693	1.00[CHB][hapmap]
rs9450694	0.94[CHB][hapmap]
rs9450697	1.00[CHB][hapmap]
rs9450698	1.00[CHB][hapmap]
rs9450699	0.91[CHB][hapmap]
rs9450700	0.91[CHB][hapmap]
rs9450708	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap]
rs9450709	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap]
rs9450716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9450717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9450740	0.90[CHB][hapmap]
rs9450749	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs9450750	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9450751	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9450756	0.90[CHB][hapmap];0.84[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2246051	SLC35A1	cis	multi-tissue	Pritchard
rs2246051	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88183600-88212800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:88183600-88226000	Weak transcription	Gastric	stomach
3	chr6:88183800-88197000	Weak transcription	NH-A	brain
4	chr6:88183800-88204200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:88183800-88210800	Weak transcription	Adipose Nuclei	Adipose
6	chr6:88183800-88211000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:88183800-88211000	Weak transcription	Brain Anterior Caudate	brain
8	chr6:88183800-88211000	Weak transcription	Thymus	Thymus
9	chr6:88183800-88211800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:88183800-88212000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:88183800-88212600	Weak transcription	Psoas Muscle	Psoas
12	chr6:88183800-88216400	Weak transcription	K562	blood
13	chr6:88183800-88219800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:88183800-88221000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr6:88183800-88221000	Weak transcription	Fetal Kidney	kidney
16	chr6:88183800-88225400	Weak transcription	Aorta	Aorta
17	chr6:88183800-88227400	Weak transcription	Right Ventricle	heart
18	chr6:88184000-88200800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:88184000-88202400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:88184000-88210800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:88184000-88211000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr6:88184000-88211000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:88184000-88218600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:88184000-88218600	Weak transcription	Brain Angular Gyrus	brain
25	chr6:88184000-88218800	Weak transcription	Brain Germinal Matrix	brain
26	chr6:88184000-88219800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:88184000-88221000	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:88184000-88224200	Weak transcription	Hela-S3	cervix
29	chr6:88184200-88211000	Weak transcription	NHDF-Ad	bronchial
30	chr6:88184200-88214800	Weak transcription	Fetal Brain Male	brain
31	chr6:88184400-88195400	Weak transcription	HepG2	liver
32	chr6:88184400-88204600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:88184400-88211200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr6:88184400-88211800	Weak transcription	Brain Substantia Nigra	brain
35	chr6:88185000-88196400	Weak transcription	HUVEC	blood vessel
36	chr6:88185800-88211400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:88186000-88211400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:88187800-88210800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr6:88188400-88202800	Weak transcription	Fetal Brain Female	brain
40	chr6:88188400-88208200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:88188400-88211000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr6:88188600-88221600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:88188800-88205400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr6:88188800-88210800	Weak transcription	Left Ventricle	heart
45	chr6:88189200-88211200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr6:88190200-88202600	Weak transcription	Osteobl	bone
47	chr6:88191200-88227400	Weak transcription	Spleen	Spleen
48	chr6:88191800-88194200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:88192400-88210200	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr6:88192800-88194200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin

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