Variant report

Variant	rs60610335
Chromosome Location	chr12:51420362-51420363
allele	C/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	chr12:51419845-51420479	U87	brain:	n/a	n/a
2	RAD21	chr12:51420040-51420514	H1-hESC	embryonic stem cell:	n/a	chr12:51420236-51420250
3	TCF3	chr12:51419858-51420491	GM12878	blood:	n/a	n/a
4	MYC	chr12:51419418-51420624	K562	blood:	n/a	chr12:51420284-51420293
5	MYC	chr12:51419575-51420564	MCF10A-Er-Src	breast:	n/a	chr12:51420284-51420293
6	EGR1	chr12:51419767-51420616	ECC-1	luminal epithelium:	n/a	chr12:51420283-51420294 chr12:51420120-51420133 chr12:51420121-51420130 chr12:51420120-51420133 chr12:51420282-51420295 chr12:51420277-51420299 chr12:51420119-51420133 chr12:51420282-51420295 chr12:51420121-51420131 chr12:51420120-51420133 chr12:51420283-51420292 chr12:51420282-51420295 chr12:51420283-51420293 chr12:51420120-51420133 chr12:51420120-51420130 chr12:51420281-51420295 chr12:51420283-51420293 chr12:51420115-51420137
7	TBP	chr12:51418482-51420562	HepG2	liver:	n/a	n/a
8	CTCF	chr12:51420260-51420410	GM12871	blood:	n/a	n/a
9	POLR2A	chr12:51419609-51420595	A549	lung:	n/a	n/a
10	HEY1	chr12:51419372-51420639	K562	blood:	n/a	chr12:51419671-51419686
11	ETS1	chr12:51419780-51420540	A549	lung:	n/a	chr12:51420119-51420130
12	YY1	chr12:51419463-51420432	H1-hESC	embryonic stem cell:	n/a	chr12:51419673-51419687 chr12:51420119-51420128 chr12:51419818-51419827
13	POLR2A	chr12:51419332-51420527	HepG2	liver:	n/a	n/a
14	POLR2A	chr12:51420226-51420498	GM12891	blood:	n/a	n/a
15	CTCF	chr12:51420187-51420501	K562	blood:	n/a	chr12:51420237-51420250
16	EP300	chr12:51419935-51420449	K562	blood:	n/a	chr12:51420120-51420136 chr12:51420119-51420128
17	CREB1	chr12:51420106-51420468	A549	lung:	n/a	n/a
18	TAF1	chr12:51419832-51420469	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:51419459-51420690	HUVEC	blood vessel:	n/a	n/a
20	CTCF	chr12:51420260-51420410	HMF	breast:	n/a	n/a
21	CTCF	chr12:51420260-51420410	GM12872	blood:	n/a	n/a
22	YY1	chr12:51419687-51420477	H1-hESC	embryonic stem cell:	n/a	chr12:51420119-51420128 chr12:51419818-51419827
23	MAX	chr12:51419237-51420765	HepG2	liver:	n/a	chr12:51420284-51420293
24	CTCF	chr12:51420280-51420430	AG04450	lung:	n/a	n/a
25	MAX	chr12:51419220-51420761	HepG2	liver:	n/a	chr12:51420284-51420293
26	CTCF	chr12:51420260-51420410	AoAF	blood vessel:	n/a	n/a
27	CREB1	chr12:51419702-51420488	A549	lung:	n/a	n/a
28	TAF1	chr12:51419351-51420512	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr12:51420250-51420520	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr12:51420320-51420470	BE2_C	brain:	n/a	n/a
31	CTCF	chr12:51420300-51420450	NHDF-neo	bronchial:	n/a	n/a
32	MYBL2	chr12:51418563-51420609	HepG2	liver:	n/a	n/a
33	CTCF	chr12:51420260-51420410	WERI-Rb-1	eye:	n/a	n/a
34	TBP	chr12:51419456-51420534	H1-hESC	embryonic stem cell:	n/a	n/a
35	SIN3AK20	chr12:51419802-51420401	PFSK-1	brain:	n/a	n/a
36	POLR2A	chr12:51419292-51420561	K562	blood:	n/a	n/a
37	POLR2A	chr12:51419274-51420729	SK-N-MC	brain:	n/a	n/a
38	FOS	chr12:51420049-51420455	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr12:51420320-51420470	HRPEpiC	eye:	n/a	n/a
40	EP300	chr12:51419978-51420452	GM12878	blood:	n/a	chr12:51420120-51420136 chr12:51420119-51420128
41	POLR2A	chr12:51419519-51420602	GM18951	blood:	n/a	n/a
42	FOS	chr12:51419993-51420408	K562	blood:	n/a	chr12:51420027-51420036
43	CTCF	chr12:51420280-51420430	HRPEpiC	eye:	n/a	n/a
44	POLR2A	chr12:51419756-51420621	MCF-7	breast:	n/a	n/a
45	SIN3A	chr12:51419252-51420492	H1-hESC	embryonic stem cell:	n/a	chr12:51419656-51419669
46	EBF1	chr12:51419983-51420523	GM12878	blood:	n/a	chr12:51420329-51420340 chr12:51420310-51420321
47	E2F6	chr12:51419529-51420569	K562	blood:	n/a	chr12:51420120-51420130 chr12:51420190-51420199
48	E2F6	chr12:51419458-51420751	A549	lung:	n/a	chr12:51420120-51420130 chr12:51420190-51420199
49	MAX	chr12:51419506-51420697	HCT-116	colon:	n/a	chr12:51420284-51420293
50	NR2C2	chr12:51419691-51420416	HepG2	liver:	n/a	chr12:51420068-51420077 chr12:51420065-51420080 chr12:51420066-51420079

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:51420343-51420393	NB4	blood:	n/a
2	chr12:51420343-51420393	GM12878	blood:	n/a
3	chr12:51420343-51420393	Hela-S3	cervix:	n/a
4	chr12:51420343-51420393	AG04450	lung:	fetal
5	chr12:51420346-51420396	HCT-116	colon:	n/a
6	chr12:51420343-51420393	HL-60	blood:	n/a
7	chr12:51420343-51420393	CMK	blood:	n/a
8	chr12:51420346-51420396	LNCaP	prostate:	n/a
9	chr12:51420343-51420393	A549	lung:	n/a
10	chr12:51420346-51420396	Hela-S3	cervix:	n/a
11	chr12:51420343-51420393	GM12891	blood:	n/a
12	chr12:51420343-51420393	BJ	skin:	n/a
13	chr12:51420346-51420396	HNPCEpiC	eye:	n/a
14	chr12:51420346-51420396	MCF-7	breast:	n/a
15	chr12:51420343-51420393	GM12892	blood:	n/a
16	chr12:51420346-51420396	NHBE	bronchial:	n/a
17	chr12:51420346-51420396	HPAEpiC	pulmonary alveolar:	n/a
18	chr12:51420346-51420396	Caco-2	colon:	n/a
19	chr12:51420346-51420396	AG09309	skin:	n/a
20	chr12:51420346-51420396	ovcar-3	ovarian:	n/a
21	chr12:51420346-51420396	HAEpiC	amniotic membrane:	n/a
22	chr12:51420343-51420393	HepG2	liver:	n/a
23	chr12:51420346-51420396	H1-hESC	embryonic stem cell:	embryo
24	chr12:51420346-51420396	Jurkat	blood:	n/a
25	chr12:51420343-51420393	NT2-D1	testis:	n/a
26	chr12:51420346-51420396	PFSK-1	brain:	n/a
27	chr12:51420346-51420396	SKMC	muscle:	n/a
28	chr12:51420346-51420396	HRE	kidney:	n/a
29	chr12:51420346-51420396	BE2_C	brain:	n/a
30	chr12:51420346-51420396	AG04450	lung:	fetal
31	chr12:51420343-51420393	NHBE	bronchial:	n/a
32	chr12:51420346-51420396	NB4	blood:	n/a
33	chr12:51420343-51420393	GM19239	blood:	n/a
34	chr12:51420343-51420393	H1-hESC	embryonic stem cell:	embryo
35	chr12:51420343-51420393	HEK293	kidney:	embryo
36	chr12:51420343-51420393	SKMC	muscle:	n/a
37	chr12:51420343-51420393	MCF10A-Er-Src	breast:	n/a
38	chr12:51420346-51420396	BJ	skin:	n/a
39	chr12:51420343-51420393	AG04449	skin:	fetal
40	chr12:51420346-51420396	PANC-1	pancreas:	n/a
41	chr12:51420346-51420396	HCF	heart:	n/a
42	chr12:51420343-51420393	K562	blood:	n/a
43	chr12:51420346-51420396	A549	lung:	n/a
44	chr12:51420343-51420393	BE2_C	brain:	n/a
45	chr12:51420346-51420396	HCM	heart:	n/a
46	chr12:51420346-51420396	SK-N-SH	brain:	n/a
47	chr12:51420346-51420396	SAEC	small airway:	n/a
48	chr12:51420346-51420396	GM19239	blood:	n/a
49	chr12:51420346-51420396	CMK	blood:	n/a
50	chr12:51420346-51420396	HCPEpiC	choroid plexus:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:51393339..51395355-chr12:51418733..51421410,2	MCF-7	breast:
2	chr12:51385408..51389476-chr12:51420028..51421870,3	MCF-7	breast:
3	chr12:51156345..51159697-chr12:51418125..51424480,11	MCF-7	breast:
4	chr12:51417420..51423779-chr12:51473917..51478493,9	MCF-7	breast:
5	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
6	chr12:51397137..51401396-chr12:51418750..51422923,7	MCF-7	breast:
7	chr12:51418513..51423622-chr12:51474378..51479071,10	MCF-7	breast:
8	chr12:51419815..51423306-chr17:56706440..56710556,3	MCF-7	breast:
9	chr12:51419463..51422870-chr12:51476162..51478400,3	K562	blood:
10	chr12:51420109..51420744-chr5:151150533..151151051,2	HCT-116	colon:
11	chr12:51418602..51423346-chr12:51439309..51444851,15	MCF-7	breast:
12	chr12:51377924..51379984-chr12:51420251..51421770,2	MCF-7	breast:
13	chr12:51418785..51420716-chr12:51421022..51423680,2	K562	blood:
14	chr12:51388022..51389545-chr12:51419948..51422038,2	MCF-7	breast:
15	chr12:51155914..51160622-chr12:51417270..51421869,9	K562	blood:
16	chr12:51419952..51421943-chr12:51475612..51477490,4	K562	blood:
17	chr12:51416659..51422801-chr12:51440164..51444812,17	MCF-7	breast:
18	chr12:51156114..51160622-chr12:51418657..51421869,11	K562	blood:
19	chr12:51316948..51319607-chr12:51419309..51421732,3	K562	blood:
20	chr12:51420182..51422992-chr12:51631104..51633893,3	MCF-7	breast:
21	chr12:51316948..51319607-chr12:51419309..51421732,2	K562	blood:
22	chr12:51398011..51404686-chr12:51416862..51423754,14	MCF-7	breast:

Variant related genes	Relation type
SLC11A2	TF binding region
SLC11A2	CpG island
ENSG00000050426	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000185432	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000145907	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11169614	1.00[AMR][1000 genomes]
rs11835513	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17124979	1.00[AMR][1000 genomes]
rs17125085	1.00[AMR][1000 genomes]
rs17125212	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17125227	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17125245	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56809906	1.00[AMR][1000 genomes]
rs56840343	1.00[AMR][1000 genomes]
rs56883422	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56979742	1.00[AMR][1000 genomes]
rs58343549	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58493263	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60089061	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60720958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60886362	0.92[AFR][1000 genomes]
rs61550892	1.00[AMR][1000 genomes]
rs7137990	1.00[AMR][1000 genomes]
rs7303962	1.00[AMR][1000 genomes]
rs7309789	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7312269	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73296205	1.00[AMR][1000 genomes]
rs73297927	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73297940	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73297966	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73298000	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73300041	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73308073	1.00[AMR][1000 genomes]
rs73308091	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73308094	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73308096	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73310009	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73310019	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73310024	1.00[AMR][1000 genomes]
rs73311252	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51417400-51420600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr12:51417400-51420800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:51417800-51420600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:51417800-51420600	Active TSS	Aorta	Aorta
5	chr12:51417800-51420800	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr12:51417800-51420800	Active TSS	Brain Angular Gyrus	brain
7	chr12:51418000-51420400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:51418000-51420400	Active TSS	NHLF	lung
9	chr12:51418000-51420600	Active TSS	Brain Anterior Caudate	brain
10	chr12:51418000-51420600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr12:51418000-51420600	Active TSS	Right Ventricle	heart
12	chr12:51418000-51420800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:51418200-51420400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:51418200-51420400	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr12:51418200-51420400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:51418200-51420400	Active TSS	Brain Cingulate Gyrus	brain
17	chr12:51418200-51420400	Active TSS	Brain Substantia Nigra	brain
18	chr12:51418200-51420400	Active TSS	K562	blood
19	chr12:51418200-51420600	Active TSS	Esophagus	oesophagus
20	chr12:51418200-51420600	Active TSS	Ovary	ovary
21	chr12:51418200-51420600	Active TSS	Psoas Muscle	Psoas
22	chr12:51418200-51420600	Active TSS	Stomach Mucosa	stomach
23	chr12:51418200-51421200	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr12:51418400-51420400	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr12:51418400-51420400	Active TSS	Fetal Intestine Large	intestine
26	chr12:51418400-51420600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:51418400-51420600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:51418400-51420600	Active TSS	Brain Hippocampus Middle	brain
29	chr12:51418400-51420600	Active TSS	Left Ventricle	heart
30	chr12:51418600-51420400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:51418600-51420400	Active TSS	Fetal Muscle Trunk	muscle
32	chr12:51418600-51420600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:51418600-51420600	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr12:51418800-51420400	Active TSS	H1 Cell Line	embryonic stem cell
35	chr12:51418800-51420400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr12:51418800-51420400	Active TSS	Fetal Brain Male	brain
37	chr12:51418800-51420400	Active TSS	Fetal Stomach	stomach
38	chr12:51418800-51420600	Active TSS	H9 Cell Line	embryonic stem cell
39	chr12:51418800-51420600	Active TSS	Thymus	Thymus
40	chr12:51418800-51420600	Active TSS	GM12878-XiMat	blood
41	chr12:51419000-51420400	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr12:51419000-51420400	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr12:51419000-51420400	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr12:51419000-51420400	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr12:51419000-51420600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr12:51419000-51420600	Flanking Active TSS	HMEC	breast
47	chr12:51419200-51420400	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr12:51419200-51420400	Active TSS	Pancreas	Pancrea
49	chr12:51419200-51420600	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr12:51419200-51420600	Active TSS	HUES64 Cell Line	embryonic stem cell

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