Variant report

Variant	rs303016
Chromosome Location	chr6:25139464-25139465
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	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
2	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
3	ATF2	chr6:25137739-25139485	GM12878	blood:	n/a	n/a
4	NFIC	chr6:25137751-25139570	GM12878	blood:	n/a	n/a
5	CEBPB	chr6:25137713-25139611	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:25136992-25139613	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr6:25137779-25139523	Hela-S3	cervix:	n/a	n/a
8	STAT3	chr6:25138218-25139612	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
9	STAT3	chr6:25139383-25139522	MCF10A-Er-Src	breast:	n/a	n/a
10	TBP	chr6:25138285-25139777	Hela-S3	cervix:	n/a	n/a
11	MEF2A	chr6:25138107-25139518	GM12878	blood:	n/a	chr6:25139225-25139239 chr6:25138248-25138263 chr6:25139092-25139109 chr6:25138248-25138265
12	IKZF1	chr6:25138087-25139480	GM12878	blood:	n/a	n/a
13	STAT3	chr6:25137751-25139674	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
14	CHD1	chr6:25138115-25139561	GM12878	blood:	n/a	n/a

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

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1002596	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs1547055	1.00[YRI][hapmap]
rs159988	0.88[JPT][hapmap]
rs167329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16890104	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1923195	0.89[CHD][hapmap]
rs2028973	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2166682	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2166683	0.88[JPT][hapmap]
rs2295737	1.00[YRI][hapmap]
rs2516577	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2894033	0.89[CHD][hapmap]
rs302966	0.88[JPT][hapmap]
rs302968	0.85[ASW][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs302969	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs302970	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs302973	0.88[JPT][hapmap]
rs302976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs302980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs302982	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs302983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs302984	0.84[CHD][hapmap]
rs302986	0.86[AMR][1000 genomes]
rs302989	0.92[CHD][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs302990	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs302991	0.88[JPT][hapmap]
rs303006	0.88[JPT][hapmap]
rs303007	0.88[JPT][hapmap]
rs303008	0.88[JPT][hapmap]
rs303009	0.88[JPT][hapmap]
rs303015	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs303017	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs303018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303022	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs303023	0.93[AMR][1000 genomes]
rs303024	0.89[ASN][1000 genomes]
rs303025	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs303026	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3792970	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs3792971	0.84[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs3792986	0.88[JPT][hapmap]
rs3812105	0.88[CHD][hapmap]
rs3818268	0.88[JPT][hapmap]
rs392852	0.88[JPT][hapmap]
rs456816	0.82[CHB][hapmap]
rs4711078	0.81[ASN][1000 genomes]
rs4712887	0.89[CHD][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap]
rs6906102	0.88[JPT][hapmap]
rs6919920	1.00[YRI][hapmap]
rs715426	0.88[JPT][hapmap]
rs9295646	0.80[CHD][hapmap]
rs9295647	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs9393613	1.00[YRI][hapmap]
rs9393617	0.88[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]

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
rs303016	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs303016	CMAH	cis	multi-tissue	Pritchard

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25135200-25140200	Active TSS	Right Atrium	heart
2	chr6:25136000-25139800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:25136200-25139600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr6:25136200-25139800	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr6:25136200-25140000	Active TSS	Aorta	Aorta
6	chr6:25136600-25139600	Active TSS	Duodenum Mucosa	Duodenum
7	chr6:25136600-25140000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:25136800-25140000	Active TSS	Ovary	ovary
9	chr6:25137000-25139800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:25137000-25140200	Active TSS	Psoas Muscle	Psoas
11	chr6:25137200-25139600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:25137200-25139600	Active TSS	Rectal Smooth Muscle	rectum
13	chr6:25137400-25139600	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr6:25137600-25139600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:25137800-25139600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:25137800-25139800	Active TSS	Brain Substantia Nigra	brain
17	chr6:25137800-25139800	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr6:25137800-25139800	Flanking Active TSS	HUVEC	blood vessel
19	chr6:25138000-25139600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr6:25138000-25139800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr6:25138000-25140200	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr6:25138200-25139600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:25138200-25139600	Active TSS	Thymus	Thymus
24	chr6:25138200-25139600	Active TSS	NHDF-Ad	bronchial
25	chr6:25138400-25139600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:25138400-25140200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:25138400-25140400	Active TSS	Fetal Intestine Large	intestine
28	chr6:25138600-25139600	Active TSS	Fetal Thymus	thymus
29	chr6:25138600-25139800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr6:25138600-25140000	Active TSS	Fetal Intestine Small	intestine
31	chr6:25138800-25139600	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr6:25138800-25139600	Active TSS	Fetal Muscle Leg	muscle
33	chr6:25138800-25139600	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr6:25138800-25139600	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr6:25138800-25139800	Weak transcription	Pancreas	Pancrea
36	chr6:25138800-25140000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr6:25138800-25140200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:25138800-25152800	Weak transcription	Lung	lung
39	chr6:25139000-25139600	Active TSS	Adipose Nuclei	Adipose
40	chr6:25139000-25139600	Active TSS	HMEC	breast
41	chr6:25139000-25139800	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr6:25139200-25139600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:25139200-25139600	Flanking Active TSS	Hela-S3	cervix
44	chr6:25139200-25139800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:25139200-25139800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:25139200-25139800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr6:25139200-25139800	Active TSS	NH-A	brain
48	chr6:25139200-25154800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr6:25139400-25139600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr6:25139400-25139600	Enhancers	Primary neutrophils fromperipheralblood	blood

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