Variant report

Variant	rs61690515
Chromosome Location	chr12:104609286-104609287
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	POLR2A	chr12:104609261-104610292	HUVEC	blood vessel:	n/a	n/a
2	RCOR1	chr12:104609265-104610494	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr12:104609272-104609723	IMR90	lung:	n/a	chr12:104609511-104609524 chr12:104609508-104609526
4	BCLAF1	chr12:104609276-104609781	GM12878	blood:	n/a	n/a
5	SP1	chr12:104609186-104610964	A549	lung:	n/a	chr12:104609481-104609490 chr12:104609480-104609492 chr12:104609874-104609886 chr12:104609875-104609884 chr12:104609482-104609491 chr12:104609481-104609491 chr12:104609481-104609495 chr12:104609481-104609491 chr12:104609480-104609492 chr12:104609906-104609920
6	E2F6	chr12:104609230-104610259	A549	lung:	n/a	chr12:104609876-104609885
7	ELF1	chr12:104609276-104609788	GM12878	blood:	n/a	chr12:104609482-104609494
8	CTCF	chr12:104609280-104609430	A549	lung:	n/a	n/a
9	GABPA	chr12:104609261-104609918	A549	lung:	n/a	chr12:104609482-104609491 chr12:104609876-104609885
10	ELF1	chr12:104609244-104610195	GM12878	blood:	n/a	chr12:104609482-104609494
11	FOXM1	chr12:104609246-104609751	GM12878	blood:	n/a	n/a
12	FOSL2	chr12:104609169-104610999	A549	lung:	n/a	n/a
13	MAX	chr12:104609073-104611142	A549	lung:	n/a	chr12:104609481-104609491
14	MXI1	chr12:104609173-104610027	IMR90	lung:	n/a	n/a
15	ZNF384	chr12:104609258-104609573	GM12878	blood:	n/a	n/a
16	SP1	chr12:104609172-104610780	A549	lung:	n/a	chr12:104609481-104609490 chr12:104609480-104609492 chr12:104609874-104609886 chr12:104609875-104609884 chr12:104609482-104609491 chr12:104609481-104609491 chr12:104609481-104609495 chr12:104609481-104609491 chr12:104609480-104609492 chr12:104609906-104609920
17	MAX	chr12:104609212-104610796	A549	lung:	n/a	chr12:104609481-104609491
18	BCL3	chr12:104609249-104610278	A549	lung:	n/a	chr12:104609876-104609889
19	REST	chr12:104609239-104610962	A549	lung:	n/a	chr12:104609481-104609494 chr12:104610882-104610895
20	CTCF	chr12:104609131-104609965	HCT-116	colon:	n/a	chr12:104609511-104609524 chr12:104609508-104609526
21	CHD1	chr12:104609017-104610017	IMR90	lung:	n/a	n/a
22	JUND	chr12:104609254-104610082	A549	lung:	n/a	n/a
23	RAD21	chr12:104609078-104609861	IMR90	lung:	n/a	chr12:104609514-104609524 chr12:104609827-104609836
24	TRIM28	chr12:104609275-104609732	K562	blood:	n/a	n/a
25	RAD21	chr12:104609285-104609722	GM12878	blood:	n/a	chr12:104609514-104609524
26	SMC3	chr12:104609282-104610299	Hela-S3	cervix:	n/a	chr12:104609878-104609888 chr12:104609510-104609524
27	TCF12	chr12:104609213-104610096	A549	lung:	n/a	n/a
28	CTCF	chr12:104609213-104609759	K562	blood:	n/a	chr12:104609511-104609524 chr12:104609508-104609526
29	FOSL2	chr12:104609259-104609766	A549	lung:	n/a	n/a
30	ATF3	chr12:104609242-104610093	A549	lung:	n/a	n/a
31	SIX5	chr12:104608844-104611017	A549	lung:	n/a	n/a
32	RAD21	chr12:104609134-104610016	HCT-116	colon:	n/a	chr12:104609863-104609876 chr12:104609514-104609524 chr12:104609827-104609836
33	ETS1	chr12:104609152-104610057	A549	lung:	n/a	chr12:104609876-104609887 chr12:104609843-104609856 chr12:104609720-104609733 chr12:104609870-104609883
34	RAD21	chr12:104609222-104609842	A549	lung:	n/a	chr12:104609514-104609524 chr12:104609827-104609836
35	CTCF	chr12:104608875-104611081	A549	lung:	n/a	chr12:104609511-104609524 chr12:104609508-104609526
36	EP300	chr12:104609174-104610183	A549	lung:	n/a	n/a
37	CTCF	chr12:104609273-104609701	A549	lung:	n/a	chr12:104609511-104609524 chr12:104609508-104609526
38	USF1	chr12:104609284-104609734	A549	lung:	n/a	chr12:104609504-104609520 chr12:104609505-104609521
39	MAZ	chr12:104609214-104610430	IMR90	lung:	n/a	chr12:104609481-104609491
40	YY1	chr12:104609275-104609886	GM12878	blood:	n/a	chr12:104609871-104609885
41	RAD21	chr12:104609186-104610058	HCT-116	colon:	n/a	chr12:104609863-104609876 chr12:104609514-104609524 chr12:104609827-104609836
42	SMARCB1	chr12:104609219-104610228	Hela-S3	cervix:	n/a	n/a
43	GATA3	chr12:104608997-104611173	A549	lung:	n/a	chr12:104610806-104610814 chr12:104609404-104609414
44	RAD21	chr12:104609139-104609903	A549	lung:	n/a	chr12:104609863-104609876 chr12:104609514-104609524 chr12:104609827-104609836
45	BCL3	chr12:104609245-104610628	A549	lung:	n/a	chr12:104609876-104609889
46	SIN3AK20	chr12:104609193-104609837	A549	lung:	n/a	n/a
47	TCF12	chr12:104609018-104611069	A549	lung:	n/a	n/a
48	STAT5A	chr12:104609268-104609732	GM12878	blood:	n/a	n/a
49	NR2F2	chr12:104609220-104609796	K562	blood:	n/a	n/a
50	EP300	chr12:104609220-104610921	A549	lung:	n/a	chr12:104610236-104610250

No.	Distal block	Cell Line	Cell type
1	chr12:104605545..104609502-chr12:104611890..104614832,4	MCF-7	breast:
2	chr12:104608375..104610840-chr12:104681920..104683609,3	MCF-7	breast:
3	chr12:104606650..104611349-chr12:104679680..104683932,8	K562	blood:
4	chr12:104606650..104616346-chr12:104679108..104687347,18	K562	blood:

Variant related genes	Relation type
TXNRD1	TF binding region
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10861184	0.83[AMR][1000 genomes]
rs11111974	0.83[AMR][1000 genomes]
rs11111975	0.83[AMR][1000 genomes]
rs11829922	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11836627	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11837739	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11838277	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299450	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12303096	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12303143	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307313	0.83[AMR][1000 genomes]
rs12320661	0.92[EUR][1000 genomes]
rs17035253	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17035296	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17807362	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35861067	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57040145	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57416848	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57718153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58729796	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59185359	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59945395	0.85[EUR][1000 genomes]
rs60264625	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7296260	0.86[ASN][1000 genomes]
rs73392529	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73392542	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73392580	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73392594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394503	0.94[EUR][1000 genomes]
rs73394521	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394563	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[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	nsv1045725	chr12:104524153-104614108	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	nsv541586	chr12:104524153-104614108	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
3	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
4	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104607800-104609400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr12:104607800-104609400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:104607800-104609800	Enhancers	NHDF-Ad	bronchial
4	chr12:104608200-104609400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:104609000-104609400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:104609000-104609400	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr12:104609000-104609400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:104609000-104609400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr12:104609000-104609400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr12:104609000-104609400	Enhancers	Fetal Kidney	kidney
11	chr12:104609000-104609400	Flanking Active TSS	A549	lung
12	chr12:104609000-104609400	Flanking Active TSS	Hela-S3	cervix
13	chr12:104609000-104609600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:104609200-104609400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:104609200-104609400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:104609200-104609400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:104609200-104609400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:104609200-104609400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:104609200-104609400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr12:104609200-104609400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:104609200-104609400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
22	chr12:104609200-104609400	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr12:104609200-104609400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr12:104609200-104609400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr12:104609200-104609400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr12:104609200-104609400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:104609200-104609400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr12:104609200-104609400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:104609200-104609400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr12:104609200-104609400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:104609200-104609400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr12:104609200-104609400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr12:104609200-104609400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:104609200-104609400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr12:104609200-104609400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:104609200-104609400	Enhancers	Brain Hippocampus Middle	brain
37	chr12:104609200-104609400	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr12:104609200-104609400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
39	chr12:104609200-104609400	Bivalent Enhancer	Fetal Stomach	stomach
40	chr12:104609200-104609400	Enhancers	Fetal Thymus	thymus
41	chr12:104609200-104609400	Enhancers	Left Ventricle	heart
42	chr12:104609200-104609400	Flanking Active TSS	Ovary	ovary
43	chr12:104609200-104609400	Enhancers	Pancreas	Pancrea
44	chr12:104609200-104609400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr12:104609200-104609400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr12:104609200-104609400	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr12:104609200-104609400	Flanking Active TSS	Thymus	Thymus
48	chr12:104609200-104609400	Active TSS	HMEC	breast
49	chr12:104609200-104609400	Flanking Active TSS	Osteobl	bone
50	chr12:104609200-104609600	Active TSS	HUES6 Cell Line	embryonic stem cell

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