Variant report

Variant	rs11168960
Chromosome Location	chr12:49668195-49668196
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:85)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:85 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49666564-49669264	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:49667500-49669360	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr12:49668099-49668530	A549	lung:	n/a	n/a
4	POLR2A	chr12:49666920-49668981	HL-60	blood:	n/a	n/a
5	POLR2A	chr12:49666418-49669114	K562	blood:	n/a	n/a
6	POLR2A	chr12:49664684-49670620	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr12:49664820-49669295	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr12:49666805-49668971	GM12878	blood:	n/a	n/a
9	GATA3	chr12:49667335-49668769	A549	lung:	n/a	n/a
10	POLR2A	chr12:49666231-49669369	PFSK-1	brain:	n/a	n/a
11	BCL3	chr12:49666451-49668725	K562	blood:	n/a	n/a
12	POLR2A	chr12:49664774-49669352	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr12:49657862-49669371	K562	blood:	n/a	n/a
14	POLR2A	chr12:49667564-49668981	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:49665913-49669127	GM12891	blood:	n/a	n/a
16	POLR2A	chr12:49666495-49668898	K562	blood:	n/a	n/a
17	POLR2A	chr12:49667234-49669281	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr12:49666416-49668859	K562	blood:	n/a	n/a
19	HEY1	chr12:49668033-49668377	HepG2	liver:	n/a	n/a
20	PML	chr12:49666402-49668372	K562	blood:	n/a	n/a
21	POLR2A	chr12:49664686-49669267	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr12:49668103-49668303	HepG2	liver:	n/a	n/a
23	POLR2A	chr12:49666991-49669296	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr12:49666483-49669149	A549	lung:	n/a	n/a
25	POLR2A	chr12:49666548-49668971	HepG2	liver:	n/a	n/a
26	HEY1	chr12:49664685-49668312	K562	blood:	n/a	n/a
27	JUND	chr12:49667022-49668754	HCT-116	colon:	n/a	chr12:49668674-49668681
28	POLR2A	chr12:49664707-49670365	U87	brain:	n/a	n/a
29	TCF12	chr12:49667682-49668877	A549	lung:	n/a	n/a
30	POLR2A	chr12:49666201-49669098	HepG2	liver:	n/a	n/a
31	POLR2A	chr12:49666527-49669299	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr12:49668131-49668549	HepG2	liver:	n/a	n/a
33	ELF1	chr12:49668172-49668618	A549	lung:	n/a	n/a
34	POLR2A	chr12:49667040-49669023	IMR90	lung:	n/a	n/a
35	POLR2A	chr12:49668077-49668363	A549	lung:	n/a	n/a
36	POLR2A	chr12:49666614-49669055	K562	blood:	n/a	n/a
37	MTA3	chr12:49668041-49668939	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:49666476-49669259	MCF-7	breast:	n/a	n/a
39	POLR2A	chr12:49666509-49670373	U87	brain:	n/a	n/a
40	POLR2A	chr12:49665844-49669180	GM12892	blood:	n/a	n/a
41	POLR2A	chr12:49665886-49669107	GM12891	blood:	n/a	n/a
42	POLR2A	chr12:49666478-49669138	HepG2	liver:	n/a	n/a
43	JUND	chr12:49668117-49668944	A549	lung:	n/a	chr12:49668674-49668681
44	POLR2A	chr12:49668077-49668252	A549	lung:	n/a	n/a
45	BCLAF1	chr12:49666390-49668252	K562	blood:	n/a	n/a
46	POLR2A	chr12:49668086-49668235	GM12878	blood:	n/a	n/a
47	POLR2A	chr12:49666384-49668538	K562	blood:	n/a	n/a
48	POLR2A	chr12:49667963-49668263	ProgFib	skin:	n/a	n/a
49	POLR2A	chr12:49667913-49668970	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr12:49658323-49670206	PFSK-1	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49667022..49671096-chr12:49685141..49687523,3	K562	blood:
2	chr12:49667825..49672911-chr12:49731373..49736764,7	K562	blood:
3	chr12:49667042..49668619-chr12:49959885..49961439,2	MCF-7	breast:
4	chr12:49667402..49669417-chr12:49680548..49682820,2	K562	blood:
5	chr12:49666275..49670972-chr12:49688443..49691988,7	K562	blood:
6	chr12:49667022..49669779-chr12:49685141..49687257,2	K562	blood:
7	chr12:49666353..49668796-chr19:796925..798586,2	K562	blood:
8	chr12:49523127..49526155-chr12:49667398..49671055,3	K562	blood:
9	chr12:49667913..49670211-chr12:49679594..49681611,2	MCF-7	breast:
10	chr12:49665854..49668915-chr12:49685671..49689413,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258232	TF binding region
ENSG00000135406	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000011304	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000123416	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11168951	0.89[ASN][1000 genomes]
rs59976042	0.83[EUR][1000 genomes]
rs60284712	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv976612	chr12:49666119-49668483	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49659200-49673600	Weak transcription	Fetal Brain Male	brain
2	chr12:49659600-49668600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:49659600-49669600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:49659600-49673600	Weak transcription	Brain Hippocampus Middle	brain
5	chr12:49659800-49668600	Weak transcription	Right Atrium	heart
6	chr12:49661000-49669800	Strong transcription	Fetal Stomach	stomach
7	chr12:49661600-49670600	Weak transcription	Psoas Muscle	Psoas
8	chr12:49662000-49668600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:49662200-49668600	Strong transcription	Primary T cells from cord blood	blood
10	chr12:49662600-49668400	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr12:49662600-49669000	Strong transcription	Fetal Muscle Leg	muscle
12	chr12:49662800-49673400	Weak transcription	Brain Anterior Caudate	brain
13	chr12:49662800-49673400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr12:49662800-49673400	Weak transcription	Brain Substantia Nigra	brain
15	chr12:49663000-49668200	Strong transcription	Fetal Muscle Trunk	muscle
16	chr12:49663000-49668400	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:49663000-49669600	Strong transcription	Thymus	Thymus
18	chr12:49663000-49669800	Strong transcription	Fetal Intestine Small	intestine
19	chr12:49663200-49668200	Strong transcription	Lung	lung
20	chr12:49663200-49668600	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr12:49663200-49668600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:49663200-49669000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:49663200-49669200	Strong transcription	Duodenum Mucosa	Duodenum
24	chr12:49663400-49668200	Strong transcription	HSMMtube	muscle
25	chr12:49663400-49668400	Strong transcription	Gastric	stomach
26	chr12:49663400-49668600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr12:49663400-49668800	Strong transcription	Spleen	Spleen
28	chr12:49663400-49669800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:49663600-49668400	Strong transcription	Aorta	Aorta
30	chr12:49663600-49669000	Strong transcription	Primary B cells from cord blood	blood
31	chr12:49663800-49669200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:49664000-49668800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:49664200-49668400	Strong transcription	NHEK	skin
34	chr12:49664200-49668600	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr12:49664200-49669800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:49664400-49668400	Strong transcription	NH-A	brain
37	chr12:49664400-49668400	Strong transcription	NHLF	lung
38	chr12:49664400-49668800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:49664400-49668800	Weak transcription	Colon Smooth Muscle	Colon
40	chr12:49664400-49669000	Strong transcription	HSMM	muscle
41	chr12:49664600-49668600	Strong transcription	HMEC	breast
42	chr12:49664600-49669600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:49665000-49668200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:49665200-49673200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:49665400-49669000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:49665400-49669600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:49665400-49673800	Weak transcription	Fetal Kidney	kidney
48	chr12:49665600-49669000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:49665600-49669000	Strong transcription	A549	lung
50	chr12:49665600-49670000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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