Variant report

Variant	rs3847694
Chromosome Location	chr12:122325820-122325821
allele	C/T
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	IRF1	chr12:122325781-122327382	K562	blood:	n/a	chr12:122326467-122326476 chr12:122326622-122326636 chr12:122326677-122326691
2	GABPA	chr12:122325657-122327323	MCF-7	breast:	n/a	n/a
3	RAD21	chr12:122325658-122327980	SK-N-SH	brain:	n/a	chr12:122327716-122327735 chr12:122327047-122327056
4	CTCF	chr12:122325636-122327917	SK-N-SH	brain:	n/a	chr12:122326573-122326586 chr12:122327723-122327731 chr12:122327719-122327735 chr12:122327713-122327734
5	JUN	chr12:122325490-122327909	K562	blood:	n/a	chr12:122326468-122326476 chr12:122326467-122326477 chr12:122326466-122326478 chr12:122326467-122326477
6	HCFC1	chr12:122325619-122327601	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr12:122325802-122327877	A549	lung:	n/a	chr12:122326573-122326586 chr12:122327723-122327731 chr12:122327719-122327735 chr12:122327713-122327734
8	RAD21	chr12:122325748-122327278	HCT-116	colon:	n/a	chr12:122327047-122327056
9	CEBPB	chr12:122325565-122325846	A549	lung:	n/a	chr12:122325674-122325685
10	MAX	chr12:122325713-122327420	HCT-116	colon:	n/a	chr12:122326467-122326476 chr12:122326565-122326572 chr12:122326561-122326576 chr12:122326559-122326574
11	MXI1	chr12:122325562-122328031	SK-N-SH	brain:	n/a	n/a
12	MYC	chr12:122325513-122327168	A549	lung:	n/a	chr12:122326467-122326476 chr12:122326565-122326572 chr12:122326561-122326576 chr12:122326559-122326574
13	PML	chr12:122325785-122327626	GM12878	blood:	n/a	n/a
14	CEBPB	chr12:122325539-122325861	HepG2	liver:	n/a	chr12:122325674-122325685
15	FOSL2	chr12:122325818-122327282	A549	lung:	n/a	chr12:122326468-122326476 chr12:122326467-122326477 chr12:122326466-122326478 chr12:122326465-122326476 chr12:122326467-122326477
16	ARID3A	chr12:122325816-122326760	HepG2	liver:	n/a	n/a
17	GATA3	chr12:122325682-122326376	SH-SY5Y	brain:	n/a	n/a
18	CTCF	chr12:122325801-122327339	HCT-116	colon:	n/a	chr12:122326573-122326586
19	RCOR1	chr12:122325691-122327600	IMR90	lung:	n/a	n/a
20	MXI1	chr12:122325807-122327936	IMR90	lung:	n/a	n/a
21	EP300	chr12:122325814-122327360	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:122325656..122327392-chr12:122459155..122461282,2	K562	blood:
2	chr12:122228836..122242951-chr12:122324438..122335797,34	K562	blood:
3	chr12:122321753..122324282-chr12:122324684..122326491,2	K562	blood:
4	chr12:122213395..122216201-chr12:122325531..122328146,2	MCF-7	breast:
5	chr12:122232032..122233517-chr12:122325701..122326925,10	MCF-7	breast:
6	chr12:122228999..122246158-chr12:122324401..122342013,93	MCF-7	breast:
7	chr12:122214229..122218603-chr12:122325636..122328202,4	MCF-7	breast:
8	chr12:122319572..122322353-chr12:122324355..122326595,2	MCF-7	breast:
9	chr12:122325518..122327854-chr12:122516363..122518486,3	K562	blood:
10	chr12:122231564..122242843-chr12:122324518..122333366,33	K562	blood:
11	chr12:122325172..122329151-chr12:122329541..122333817,7	MCF-7	breast:
12	chr12:122228992..122246947-chr12:122322343..122339116,70	MCF-7	breast:
13	chr12:122325289..122328252-chr12:122355129..122358130,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256950	TF binding region
PSMD9	TF binding region
ENSG00000188735	Chromatin interaction
ENSG00000272849	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000139718	Chromatin interaction
ENSG00000175727	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000110987	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10431199	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs10770186	0.82[CEU][hapmap]
rs10840624	0.83[CHB][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap]
rs10840630	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs10840631	0.96[CEU][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs10840632	0.96[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs10840637	0.89[CEU][hapmap]
rs11043216	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11043218	0.91[CHB][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap]
rs11043229	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11043233	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs11043237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11043241	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11043242	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11043243	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs11043251	0.96[CEU][hapmap]
rs11043255	1.00[JPT][hapmap]
rs11043271	0.96[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs11043285	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs11043286	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs11043288	0.80[MEX][hapmap];0.82[TSI][hapmap]
rs1154514	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs11612028	0.96[CEU][hapmap]
rs11615980	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12229068	0.80[ASN][1000 genomes]
rs12817066	0.85[EUR][1000 genomes]
rs12824593	0.96[CEU][hapmap]
rs12827452	0.82[EUR][1000 genomes]
rs1610041	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1720033	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs1720037	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs2707058	0.82[CHD][hapmap]
rs35892692	1.00[ASN][1000 genomes]
rs3887885	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4069668	0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs61954311	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486780	1.00[ASN][1000 genomes]
rs6486782	0.82[CEU][hapmap]
rs7132055	0.96[CEU][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs7137218	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.98[GIH][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7309024	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954584	0.85[MEX][hapmap]
rs7958406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7970565	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971538	0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3847694	RP11-7M8.2	cis	Muscle Skeletal	GTEx
rs3847694	BCL7A	cis	Muscle Skeletal	GTEx
rs3847694	WDR66	cis	cerebellum	SCAN
rs3847694	HPD	cis	Muscle Skeletal	GTEx
rs3847694	CCDC60	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122321400-122326000	Weak transcription	Right Atrium	heart
2	chr12:122321400-122326200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:122321400-122326200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:122321800-122326000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:122322000-122326000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:122323400-122326000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:122325600-122326000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:122325600-122326000	Enhancers	Liver	Liver
9	chr12:122325600-122326200	Flanking Active TSS	A549	lung
10	chr12:122325600-122326400	Flanking Active TSS	Dnd41	blood
11	chr12:122325800-122326000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:122325800-122326000	Enhancers	Primary B cells from peripheral blood	blood
13	chr12:122325800-122326000	Enhancers	Primary T cells from cord blood	blood
14	chr12:122325800-122326000	Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr12:122325800-122326000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:122325800-122326000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr12:122325800-122326000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr12:122325800-122326000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr12:122325800-122326000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr12:122325800-122326000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:122325800-122326000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr12:122325800-122326000	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr12:122325800-122326000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr12:122325800-122326000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:122325800-122326000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:122325800-122326000	Enhancers	Adipose Nuclei	Adipose
27	chr12:122325800-122326000	Enhancers	Brain Angular Gyrus	brain
28	chr12:122325800-122326000	Enhancers	Brain Anterior Caudate	brain
29	chr12:122325800-122326000	Active TSS	Brain Cingulate Gyrus	brain
30	chr12:122325800-122326000	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr12:122325800-122326000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:122325800-122326000	Enhancers	Colon Smooth Muscle	Colon
33	chr12:122325800-122326000	Enhancers	Duodenum Mucosa	Duodenum
34	chr12:122325800-122326000	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr12:122325800-122326000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr12:122325800-122326000	Enhancers	Fetal Kidney	kidney
37	chr12:122325800-122326000	Active TSS	Rectal Smooth Muscle	rectum
38	chr12:122325800-122326000	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr12:122325800-122326000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr12:122325800-122326000	Enhancers	HMEC	breast
41	chr12:122325800-122326000	Enhancers	HSMMtube	muscle
42	chr12:122325800-122326000	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr12:122325800-122326000	Enhancers	NHDF-Ad	bronchial
44	chr12:122325800-122326200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:122325800-122326200	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr12:122325800-122326400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:122325800-122326400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:122325800-122326400	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr12:122325800-122326400	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr12:122325800-122326400	Flanking Active TSS	GM12878-XiMat	blood

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