Variant report

Variant	rs2028973
Chromosome Location	chr6:25138627-25138628
allele	A/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	POLR2A	chr6:25138223-25138841	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:25138023-25139021	GM12892	blood:	n/a	n/a
3	CTCF	chr6:25138500-25138650	HBMEC	blood vessel:	n/a	n/a
4	STAT3	chr6:25138331-25139625	GM12878	blood:	n/a	chr6:25139524-25139538 chr6:25139527-25139536 chr6:25139363-25139371 chr6:25139366-25139389 chr6:25139526-25139535 chr6:25139188-25139199 chr6:25138559-25138566 chr6:25139182-25139193
5	MYC	chr6:25138377-25139321	MCF10A-Er-Src	breast:	n/a	n/a
6	TCF12	chr6:25138111-25139011	SK-N-SH	brain:	n/a	n/a
7	SMC3	chr6:25138280-25139036	Hela-S3	cervix:	n/a	n/a
8	IRF1	chr6:25138540-25139435	K562	blood:	n/a	chr6:25139183-25139197 chr6:25139185-25139199 chr6:25139177-25139198 chr6:25139188-25139201 chr6:25139189-25139199 chr6:25139182-25139193 chr6:25139188-25139199 chr6:25139181-25139192 chr6:25139187-25139201 chr6:25139187-25139198 chr6:25139182-25139195 chr6:25139182-25139195 chr6:25139181-25139201 chr6:25139182-25139195 chr6:25139187-25139200 chr6:25139183-25139193 chr6:25139182-25139196 chr6:25139183-25139200 chr6:25139186-25139200 chr6:25139188-25139200 chr6:25139189-25139203 chr6:25139182-25139195 chr6:25139179-25139193
9	CTCF	chr6:25138527-25138671	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:25138179-25139227	SK-N-SH	brain:	n/a	n/a
11	MTA3	chr6:25137947-25139435	GM12878	blood:	n/a	n/a
12	CTCF	chr6:25138540-25138690	HFF-Myc	foreskin:	n/a	n/a
13	POLR2A	chr6:25137735-25138940	GM12892	blood:	n/a	n/a
14	IRF1	chr6:25138550-25138707	K562	blood:	n/a	n/a
15	STAT3	chr6:25138238-25139673	MCF10A-Er-Src	breast:	n/a	chr6:25139524-25139538 chr6:25139527-25139536 chr6:25139363-25139371 chr6:25139366-25139389 chr6:25139526-25139535 chr6:25139188-25139199 chr6:25138559-25138566 chr6:25139182-25139193
16	MAZ	chr6:25138151-25139330	GM12878	blood:	n/a	n/a
17	CTCF	chr6:25138500-25138650	GM12864	blood:	n/a	n/a
18	CTCF	chr6:25138520-25138670	HCPEpiC	choroid plexus:	n/a	n/a
19	BCL11A	chr6:25138247-25138752	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:25137762-25138962	GM12878	blood:	n/a	n/a
21	CTCF	chr6:25138560-25138710	AG04450	lung:	n/a	n/a
22	FOXM1	chr6:25138126-25139429	GM12878	blood:	n/a	n/a
23	CTCF	chr6:25138500-25138650	HCPEpiC	choroid plexus:	n/a	n/a
24	POLR2A	chr6:25137737-25139277	GM12892	blood:	n/a	n/a
25	POU2F2	chr6:25138387-25138778	GM12891	blood:	n/a	n/a
26	CTCF	chr6:25138500-25138650	HPAF	blood vessel:	n/a	n/a
27	CTCF	chr6:25138520-25138670	HPAF	blood vessel:	n/a	n/a
28	POLR2A	chr6:25138263-25138951	U87	brain:	n/a	n/a
29	SPI1	chr6:25138279-25138807	GM12891	blood:	n/a	chr6:25138561-25138568
30	SPI1	chr6:25138200-25138767	GM12878	blood:	n/a	chr6:25138561-25138568
31	CTCF	chr6:25138491-25138683	A549	lung:	n/a	n/a
32	RAD21	chr6:25138360-25139141	Hela-S3	cervix:	n/a	chr6:25138735-25138747
33	CTCF	chr6:25138480-25138630	GM12878	blood:	n/a	n/a
34	CTCF	chr6:25138522-25138677	GM12892	blood:	n/a	n/a
35	CTCF	chr6:25138500-25138650	Hela-S3	cervix:	n/a	n/a
36	TAF1	chr6:25138189-25138808	GM12878	blood:	n/a	n/a
37	MAX	chr6:25138377-25138932	SK-N-SH	brain:	n/a	n/a
38	ATF2	chr6:25137739-25139485	GM12878	blood:	n/a	n/a
39	POLR2A	chr6:25138286-25139307	MCF10A-Er-Src	breast:	n/a	n/a
40	CTCF	chr6:25138529-25138656	MCF-7	breast:	n/a	n/a
41	PAX5	chr6:25138353-25139197	GM12878	blood:	n/a	chr6:25139184-25139193 chr6:25138559-25138568 chr6:25138579-25138588
42	POLR2A	chr6:25137855-25138983	Raji	blood:	n/a	n/a
43	CTCF	chr6:25138560-25138710	GM12866	blood:	n/a	n/a
44	RELA	chr6:25137765-25139153	GM15510	blood:	n/a	n/a
45	CTCF	chr6:25138560-25138710	HCM	heart:	n/a	n/a
46	SPI1	chr6:25137995-25139033	GM12878	blood:	n/a	chr6:25138561-25138568
47	CEBPB	chr6:25137782-25139143	IMR90	lung:	n/a	n/a
48	NFIC	chr6:25137751-25139570	GM12878	blood:	n/a	n/a
49	POLR2A	chr6:25138234-25139009	GM12878	blood:	n/a	n/a
50	ZNF143	chr6:25138265-25139053	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000219682	TF binding region
CMAHP	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1002596	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs159988	1.00[ASW][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs167329	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16890104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2166682	0.88[JPT][hapmap]
rs2166683	0.88[JPT][hapmap]
rs302966	0.88[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs302973	0.86[CHD][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap]
rs302976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs302980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs302983	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs302989	0.81[CHD][hapmap]
rs302990	0.82[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs302991	0.81[ASW][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap]
rs303000	0.87[CHD][hapmap]
rs303004	0.90[AFR][1000 genomes]
rs303006	1.00[ASW][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs303007	0.88[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs303008	0.88[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs303009	1.00[ASW][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs303015	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs303016	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs303017	0.86[ASN][1000 genomes]
rs303018	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs303024	0.98[ASN][1000 genomes]
rs303026	1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3792970	0.88[JPT][hapmap]
rs3792971	0.88[CHD][hapmap];0.88[JPT][hapmap]
rs3792986	0.88[JPT][hapmap]
rs3812105	0.80[CHD][hapmap]
rs3818268	0.88[JPT][hapmap]
rs391626	0.86[AFR][1000 genomes]
rs392852	0.92[CHD][hapmap];0.88[JPT][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs398672	0.82[AFR][1000 genomes]
rs420369	0.86[AFR][1000 genomes]
rs456816	0.82[CHB][hapmap]
rs57304238	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57796643	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6906102	0.88[JPT][hapmap]
rs715426	0.88[JPT][hapmap]
rs9295646	0.84[CHD][hapmap]
rs9295647	0.88[CHD][hapmap];0.88[JPT][hapmap]
rs9393617	0.92[CHD][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv470806	chr6:25082262-25156197	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv462662	chr6:25084718-25165486	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv601166	chr6:25084718-25165486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv1798120	chr6:25136860-25149538	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2028973	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs2028973	CMAH	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25135200-25140200	Active TSS	Right Atrium	heart
2	chr6:25136000-25138800	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr6:25136000-25139800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:25136200-25139000	Active TSS	Left Ventricle	heart
5	chr6:25136200-25139600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr6:25136200-25139800	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr6:25136200-25140000	Active TSS	Aorta	Aorta
8	chr6:25136400-25139200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr6:25136400-25139400	Active TSS	Brain Hippocampus Middle	brain
10	chr6:25136600-25139400	Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr6:25136600-25139600	Active TSS	Duodenum Mucosa	Duodenum
12	chr6:25136600-25140000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:25136800-25138800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:25136800-25138800	Active TSS	Sigmoid Colon	Sigmoid Colon
15	chr6:25136800-25139000	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr6:25136800-25139000	Flanking Active TSS	Liver	Liver
17	chr6:25136800-25139000	Flanking Active TSS	Osteobl	bone
18	chr6:25136800-25139400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr6:25136800-25139400	Active TSS	Brain Anterior Caudate	brain
20	chr6:25136800-25139400	Active TSS	Right Ventricle	heart
21	chr6:25136800-25140000	Active TSS	Ovary	ovary
22	chr6:25137000-25139000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:25137000-25139400	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr6:25137000-25139400	Active TSS	Colonic Mucosa	Colon
25	chr6:25137000-25139400	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr6:25137000-25139800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:25137000-25140200	Active TSS	Psoas Muscle	Psoas
28	chr6:25137200-25139600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:25137200-25139600	Active TSS	Rectal Smooth Muscle	rectum
30	chr6:25137400-25139400	Active TSS	Primary T cells fromperipheralblood	blood
31	chr6:25137400-25139400	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr6:25137400-25139400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr6:25137400-25139400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr6:25137400-25139400	Active TSS	Colon Smooth Muscle	Colon
35	chr6:25137400-25139400	Active TSS	GM12878-XiMat	blood
36	chr6:25137400-25139600	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr6:25137600-25139400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:25137600-25139400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:25137600-25139400	Weak transcription	Fetal Heart	heart
40	chr6:25137600-25139600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:25137800-25138800	Flanking Active TSS	Hela-S3	cervix
42	chr6:25137800-25139000	Active TSS	Esophagus	oesophagus
43	chr6:25137800-25139400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:25137800-25139600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:25137800-25139800	Active TSS	Brain Substantia Nigra	brain
46	chr6:25137800-25139800	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr6:25137800-25139800	Flanking Active TSS	HUVEC	blood vessel
48	chr6:25138000-25138800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:25138000-25139400	Active TSS	Fetal Kidney	kidney
50	chr6:25138000-25139600	Active TSS	Primary T regulatory cells fromperipheralblood	blood

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