Variant report

Variant	rs3796160
Chromosome Location	chr3:194906614-194906615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr3:194906431-194906631	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:194906542-194906774	K562	blood:	n/a	n/a
3	FOS	chr3:194906407-194906662	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr3:194906377-194906738	Hela-S3	cervix:	n/a	n/a
5	ESR1	chr3:194906018-194906776	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr3:194906457-194906625	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr3:194906347-194906780	MCF-7	breast:	n/a	n/a
8	STAT3	chr3:194906310-194906721	MCF10A-Er-Src	breast:	n/a	n/a
9	PRDM1	chr3:194906312-194906794	Hela-S3	cervix:	n/a	chr3:194906590-194906603 chr3:194906583-194906598 chr3:194906618-194906627 chr3:194906616-194906631
10	FOS	chr3:194906311-194906698	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr3:194906294-194906802	ECC-1	luminal epithelium:	n/a	n/a
12	CEBPB	chr3:194906432-194906661	K562	blood:	n/a	n/a
13	MAX	chr3:194906207-194906788	ECC-1	luminal epithelium:	n/a	n/a
14	ESR1	chr3:194906045-194906624	ECC-1	luminal epithelium:	n/a	n/a
15	RCOR1	chr3:194906425-194906693	Hela-S3	cervix:	n/a	n/a
16	RCOR1	chr3:194906365-194906866	K562	blood:	n/a	n/a
17	CEBPB	chr3:194906388-194906744	K562	blood:	n/a	n/a
18	POLR2A	chr3:194906315-194906685	MCF10A-Er-Src	breast:	n/a	n/a
19	CEBPB	chr3:194906323-194906784	ECC-1	luminal epithelium:	n/a	n/a
20	STAT3	chr3:194906432-194906711	MCF10A-Er-Src	breast:	n/a	n/a
21	ESR1	chr3:194906003-194906741	ECC-1	luminal epithelium:	n/a	n/a
22	MAZ	chr3:194906457-194906690	K562	blood:	n/a	n/a
23	STAT3	chr3:194906425-194906652	MCF10A-Er-Src	breast:	n/a	n/a
24	TCF12	chr3:194906235-194906828	ECC-1	luminal epithelium:	n/a	n/a
25	STAT3	chr3:194906437-194906651	MCF10A-Er-Src	breast:	n/a	n/a
26	FOS	chr3:194906339-194906684	MCF10A-Er-Src	breast:	n/a	n/a
27	ELK1	chr3:194906445-194906631	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr3:194906392-194906681	K562	blood:	n/a	n/a
29	TCF7L2	chr3:194906335-194906676	Hela-S3	cervix:	n/a	n/a
30	TBP	chr3:194906385-194906654	Hela-S3	cervix:	n/a	n/a
31	TBL1XR1	chr3:194906550-194906743	K562	blood:	n/a	n/a
32	UBTF	chr3:194906451-194906635	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:194905664..194908891-chr3:194914398..194916423,3	K562	blood:
2	chr3:194897295..194902185-chr3:194905804..194909141,6	K562	blood:
3	chr3:194897295..194902438-chr3:194905804..194908922,5	K562	blood:
4	chr3:194873006..194875023-chr3:194905477..194907059,2	K562	blood:

No data

Variant related genes	Relation type
XXYLT1	TF binding region
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11919965	0.84[CHD][hapmap];0.91[GIH][hapmap]
rs11925335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12496868	0.83[EUR][1000 genomes]
rs12497906	0.84[CHD][hapmap];0.90[GIH][hapmap]
rs13064053	1.00[ASN][1000 genomes]
rs1874102	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1961324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410805	0.89[EUR][1000 genomes]
rs56283237	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59190596	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781962	0.82[YRI][hapmap]
rs6810043	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628353	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs9825199	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9826142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856486	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9870185	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870684	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879463	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
10	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
12	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
13	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
14	nsv1009120	chr3:194874494-194974672	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription 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	21 gene(s)	inside rSNPs	diseases
17	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194884800-194908800	Weak transcription	Thymus	Thymus
2	chr3:194892400-194907400	Weak transcription	HSMMtube	muscle
3	chr3:194896600-194908000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:194896600-194909200	Weak transcription	Pancreas	Pancrea
5	chr3:194901200-194908600	Weak transcription	Fetal Heart	heart
6	chr3:194901600-194909000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:194901800-194906800	Weak transcription	HepG2	liver
8	chr3:194902400-194906800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:194903000-194907400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:194903000-194909000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:194903000-194909000	Weak transcription	Ovary	ovary
12	chr3:194903000-194915200	Weak transcription	Brain Substantia Nigra	brain
13	chr3:194903200-194906800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr3:194903200-194906800	Enhancers	Rectal Smooth Muscle	rectum
15	chr3:194903200-194909000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:194903200-194909000	Weak transcription	Fetal Intestine Small	intestine
17	chr3:194903200-194915000	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:194903400-194908200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:194903400-194908600	Weak transcription	HSMM	muscle
20	chr3:194903600-194908800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:194903600-194909000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:194903600-194909000	Weak transcription	Brain Anterior Caudate	brain
23	chr3:194903800-194906800	Enhancers	HUVEC	blood vessel
24	chr3:194903800-194908000	Weak transcription	Osteobl	bone
25	chr3:194903800-194908600	Enhancers	Colon Smooth Muscle	Colon
26	chr3:194903800-194908800	Weak transcription	Fetal Kidney	kidney
27	chr3:194904000-194906800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:194904000-194907200	Weak transcription	NH-A	brain
29	chr3:194904000-194908800	Weak transcription	Fetal Brain Female	brain
30	chr3:194904200-194907200	Weak transcription	Small Intestine	intestine
31	chr3:194904200-194908400	Weak transcription	Fetal Lung	lung
32	chr3:194904400-194907600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr3:194904400-194908200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:194904400-194908400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr3:194904600-194907400	Weak transcription	NHLF	lung
36	chr3:194904600-194907600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:194904600-194908000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:194904600-194908200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:194904600-194908200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:194904600-194908400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:194904600-194916400	Weak transcription	Right Atrium	heart
42	chr3:194904800-194908200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr3:194904800-194908200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:194904800-194908600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:194905000-194908000	Weak transcription	Fetal Stomach	stomach
46	chr3:194905000-194908800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr3:194905400-194907200	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr3:194905400-194907400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr3:194905600-194906800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:194905600-194907000	Enhancers	Monocytes-CD14+_RO01746	blood

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