Variant report

Variant	rs17270986
Chromosome Location	chr3:98518072-98518073
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	chr3:98516179-98518840	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:98500239-98520630	U87	brain:	n/a	n/a
3	POLR2A	chr3:98518065-98518082	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:98517312-98518676	A549	lung:	n/a	n/a
5	BCL3	chr3:98517907-98518545	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:98517264-98518824	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr3:98517699-98518596	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr3:98518043-98518099	ProgFib	skin:	n/a	n/a
9	POLR2A	chr3:98517342-98518127	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:98500581-98518912	U87	brain:	n/a	n/a
11	POLR2A	chr3:98500433-98518912	U87	brain:	n/a	n/a
12	RAD21	chr3:98517236-98518805	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98505121..98508904-chr3:98514678..98518486,3	MCF-7	breast:

Variant related genes	Relation type
ST3GAL6	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1062196	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs12054181	0.82[CHB][hapmap]
rs1440150	0.82[CHD][hapmap]
rs1837500	0.82[CHB][hapmap]
rs1866677	0.81[CHB][hapmap]
rs1866678	0.82[CHB][hapmap]
rs2119187	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2119188	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs2246861	0.82[CHB][hapmap]
rs2439222	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2439223	0.82[CHB][hapmap]
rs2439224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2439231	0.82[CHB][hapmap]
rs2439236	0.82[CHB][hapmap]
rs2454673	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs2454682	0.82[CHD][hapmap]
rs2454685	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2470825	0.82[CHB][hapmap]
rs2470857	0.82[CHB][hapmap]
rs2470859	0.82[CHB][hapmap]
rs2470861	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs2470867	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2470869	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2470881	0.82[CHB][hapmap]
rs2470885	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs3755576	0.80[CHD][hapmap]
rs6782630	0.82[CHB][hapmap]
rs6785935	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs9289683	0.82[CHB][hapmap]
rs9811860	0.82[CHB][hapmap]
rs9814819	0.82[CHB][hapmap]
rs9823430	0.82[CHB][hapmap]
rs9835142	0.82[CHB][hapmap]
rs9843214	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs9852950	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs9873932	0.82[CHB][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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17270986	DCBLD2	cis	parietal	SCAN
rs17270986	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL
rs17270986	IMPG2	cis	cerebellum	SCAN
rs17270986	ST3GAL6	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
2	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
4	chr3:98502200-98519800	Weak transcription	Fetal Kidney	kidney
5	chr3:98502200-98523800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:98502400-98523800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:98503400-98518200	Weak transcription	Ovary	ovary
8	chr3:98503400-98576400	Weak transcription	Gastric	stomach
9	chr3:98503600-98523800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:98504600-98519400	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
12	chr3:98505000-98525600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:98505400-98518400	Weak transcription	Fetal Thymus	thymus
14	chr3:98505400-98523800	Weak transcription	Pancreas	Pancrea
15	chr3:98505400-98524400	Weak transcription	Thymus	Thymus
16	chr3:98505800-98524600	Weak transcription	Psoas Muscle	Psoas
17	chr3:98506400-98519400	Weak transcription	Brain Anterior Caudate	brain
18	chr3:98506400-98524400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:98506800-98523800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:98507800-98518200	Weak transcription	Right Ventricle	heart
21	chr3:98507800-98529000	Weak transcription	Brain Substantia Nigra	brain
22	chr3:98508000-98519600	Weak transcription	Fetal Lung	lung
23	chr3:98508000-98524600	Weak transcription	GM12878-XiMat	blood
24	chr3:98508200-98524600	Weak transcription	Fetal Heart	heart
25	chr3:98511400-98518400	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:98512200-98521000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:98512400-98520800	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr3:98512800-98520400	Strong transcription	HSMM	muscle
29	chr3:98513000-98520800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:98513000-98524400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:98513400-98520600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:98513400-98520800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:98513400-98520800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:98513400-98523800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr3:98513600-98520800	Strong transcription	NH-A	brain
36	chr3:98513600-98536600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr3:98513600-98539200	Weak transcription	Colonic Mucosa	Colon
38	chr3:98513800-98518200	Weak transcription	Lung	lung
39	chr3:98513800-98520600	Strong transcription	A549	lung
40	chr3:98513800-98520800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:98513800-98520800	Strong transcription	Osteobl	bone
42	chr3:98513800-98521000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:98513800-98524400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:98513800-98525400	Weak transcription	Esophagus	oesophagus
45	chr3:98513800-98526000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:98514000-98519000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:98514000-98520000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:98514000-98520600	Strong transcription	NHDF-Ad	bronchial
49	chr3:98514400-98518200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:98514600-98518200	Weak transcription	Fetal Stomach	stomach

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