Variant report

Variant	rs3796133
Chromosome Location	chr3:98517843-98517844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:98517767-98517956	LNCaP	prostate:	n/a	n/a
2	POLR2A	chr3:98517611-98517879	HUVEC	blood vessel:	n/a	n/a
3	CTCF	chr3:98517800-98517950	BE2_C	brain:	n/a	n/a
4	CTCF	chr3:98517780-98517930	GM12878	blood:	n/a	n/a
5	SMC3	chr3:98517695-98518023	GM12878	blood:	n/a	n/a
6	CTCF	chr3:98517800-98517950	GM12873	blood:	n/a	n/a
7	POLR2A	chr3:98517716-98517912	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr3:98517803-98517945	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:98516179-98518840	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:98500239-98520630	U87	brain:	n/a	n/a
11	RAD21	chr3:98517725-98517951	GM12878	blood:	n/a	n/a
12	RAD21	chr3:98517746-98517983	SK-N-SH_RA	brain:	n/a	n/a
13	CTCF	chr3:98517720-98517870	GM12864	blood:	n/a	n/a
14	CTCF	chr3:98517780-98517930	GM12864	blood:	n/a	n/a
15	RAD21	chr3:98517758-98518023	SK-N-SH_RA	brain:	n/a	n/a
16	POLR2A	chr3:98517312-98518676	A549	lung:	n/a	n/a
17	CTCF	chr3:98517820-98517970	GM12874	blood:	n/a	n/a
18	CTCF	chr3:98517800-98517950	GM12865	blood:	n/a	n/a
19	CTCF	chr3:98517808-98517928	Kidney_OC	kidney:	n/a	n/a
20	POLR2A	chr3:98517264-98518824	SK-N-SH	brain:	n/a	n/a
21	CTCF	chr3:98517780-98517930	GM12871	blood:	n/a	n/a
22	CTCF	chr3:98517805-98517940	GM13977	blood:	n/a	n/a
23	RAD21	chr3:98517683-98518037	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:98517699-98518596	HUVEC	blood vessel:	n/a	n/a
25	CTCF	chr3:98517780-98517930	GM12865	blood:	n/a	n/a
26	POLR2A	chr3:98517342-98518127	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:98500581-98518912	U87	brain:	n/a	n/a
28	RAD21	chr3:98517728-98517981	GM12878	blood:	n/a	n/a
29	ZNF143	chr3:98517742-98518010	GM12878	blood:	n/a	n/a
30	CTCF	chr3:98517780-98517930	GM12874	blood:	n/a	n/a
31	CTCF	chr3:98517685-98518049	GM12878	blood:	n/a	n/a
32	CTCF	chr3:98517819-98517948	GM10266	blood:	n/a	n/a
33	POLR2A	chr3:98500433-98518912	U87	brain:	n/a	n/a
34	CTCF	chr3:98517781-98517987	LNCaP	prostate:	n/a	n/a
35	CTCF	chr3:98517760-98517910	HPAF	blood vessel:	n/a	n/a
36	RAD21	chr3:98517236-98518805	SK-N-SH	brain:	n/a	n/a
37	CTCF	chr3:98517800-98517950	GM12872	blood:	n/a	n/a
38	CTCF	chr3:98517800-98517950	GM12875	blood:	n/a	n/a

No data

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

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

No data

Variant related genes	Relation type
ST3GAL6	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10084679	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12330381	0.85[AMR][1000 genomes]
rs13317610	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13318960	0.85[AMR][1000 genomes]
rs13320266	0.88[ASN][1000 genomes]
rs13320890	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13322253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28417568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429424	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28489284	1.00[ASW][hapmap];0.90[GIH][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28528154	0.85[AMR][1000 genomes]
rs28650813	0.85[AMR][1000 genomes]
rs56172805	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs56857413	0.82[ASN][1000 genomes]
rs57962467	0.82[ASN][1000 genomes]
rs59906228	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72932691	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72932700	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72934623	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72934641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72938577	0.82[ASN][1000 genomes]
rs9289699	0.85[AMR][1000 genomes]
rs9289700	0.85[AMR][1000 genomes]
rs9810407	0.88[ASN][1000 genomes]
rs9812438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818215	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9833945	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9836437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9836915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9838166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9838238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9838706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839559	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9848335	0.85[AMR][1000 genomes]
rs9848583	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9862660	1.00[CEU][hapmap];1.00[CHB][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]
rs9870500	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9870940	0.85[AMR][1000 genomes]
rs9879302	0.85[AMR][1000 genomes]
rs9883751	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]

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

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
3	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
5	chr3:98502200-98519800	Weak transcription	Fetal Kidney	kidney
6	chr3:98502200-98523800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:98502400-98523800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:98503400-98518200	Weak transcription	Ovary	ovary
9	chr3:98503400-98576400	Weak transcription	Gastric	stomach
10	chr3:98503600-98523800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:98504600-98519400	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
13	chr3:98505000-98525600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:98505400-98518400	Weak transcription	Fetal Thymus	thymus
15	chr3:98505400-98523800	Weak transcription	Pancreas	Pancrea
16	chr3:98505400-98524400	Weak transcription	Thymus	Thymus
17	chr3:98505800-98524600	Weak transcription	Psoas Muscle	Psoas
18	chr3:98506200-98518000	Weak transcription	Fetal Intestine Large	intestine
19	chr3:98506400-98519400	Weak transcription	Brain Anterior Caudate	brain
20	chr3:98506400-98524400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:98506800-98523800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:98507800-98518200	Weak transcription	Right Ventricle	heart
23	chr3:98507800-98529000	Weak transcription	Brain Substantia Nigra	brain
24	chr3:98508000-98519600	Weak transcription	Fetal Lung	lung
25	chr3:98508000-98524600	Weak transcription	GM12878-XiMat	blood
26	chr3:98508200-98524600	Weak transcription	Fetal Heart	heart
27	chr3:98511400-98518400	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:98512200-98521000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:98512400-98520800	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr3:98512800-98520400	Strong transcription	HSMM	muscle
31	chr3:98513000-98520800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:98513000-98524400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:98513400-98520600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:98513400-98520800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:98513400-98520800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:98513400-98523800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:98513600-98520800	Strong transcription	NH-A	brain
38	chr3:98513600-98536600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr3:98513600-98539200	Weak transcription	Colonic Mucosa	Colon
40	chr3:98513800-98518200	Weak transcription	Lung	lung
41	chr3:98513800-98520600	Strong transcription	A549	lung
42	chr3:98513800-98520800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:98513800-98520800	Strong transcription	Osteobl	bone
44	chr3:98513800-98521000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:98513800-98524400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr3:98513800-98525400	Weak transcription	Esophagus	oesophagus
47	chr3:98513800-98526000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr3:98514000-98519000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:98514000-98520000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:98514000-98520600	Strong transcription	NHDF-Ad	bronchial

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