Variant report

Variant	rs4322502
Chromosome Location	chr12:10365345-10365346
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	chr12:10364752-10365719	HCT-116	colon:	n/a	n/a
2	HA-E2F1	chr12:10364714-10365642	MCF-7	breast:	n/a	chr12:10365422-10365431 chr12:10365446-10365455 chr12:10365444-10365453
3	BHLHE40	chr12:10364219-10365690	HepG2	liver:	n/a	chr12:10364402-10364415 chr12:10364403-10364412 chr12:10364404-10364413 chr12:10364404-10364413 chr12:10364398-10364419
4	JUND	chr12:10364713-10365544	Hela-S3	cervix:	n/a	chr12:10364966-10364974 chr12:10365426-10365435 chr12:10365445-10365454 chr12:10365421-10365430
5	MXI1	chr12:10364703-10367409	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr12:10364739-10366590	HepG2	liver:	n/a	n/a
7	BHLHE40	chr12:10364754-10365439	GM12878	blood:	n/a	n/a
8	FOXA1	chr12:10365017-10365452	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr12:10364826-10365602	HepG2	liver:	n/a	n/a
10	KAP1	chr12:10364631-10365409	U2OS	brain:	n/a	n/a
11	SIN3AK20	chr12:10364626-10365854	HCT-116	colon:	n/a	n/a
12	POLR2A	chr12:10364743-10368315	Hela-S3	cervix:	n/a	n/a
13	CREB1	chr12:10364826-10365782	H1-hESC	embryonic stem cell:	n/a	chr12:10365443-10365456
14	MXI1	chr12:10364694-10366620	Hela-S3	cervix:	n/a	n/a
15	CREB1	chr12:10364729-10366638	GM12878	blood:	n/a	chr12:10365443-10365456
16	CHD1	chr12:10365043-10366897	H1-hESC	embryonic stem cell:	n/a	chr12:10365423-10365433
17	TCF12	chr12:10364727-10365845	ECC-1	luminal epithelium:	n/a	n/a
18	USF2	chr12:10364802-10365554	Hela-S3	cervix:	n/a	n/a
19	ATF2	chr12:10364755-10365581	H1-hESC	embryonic stem cell:	n/a	chr12:10365444-10365455
20	TBL1XR1	chr12:10364794-10365593	K562	blood:	n/a	n/a
21	TEAD4	chr12:10364764-10365690	ECC-1	luminal epithelium:	n/a	n/a
22	SIX5	chr12:10364606-10365562	A549	lung:	n/a	n/a
23	JUN	chr12:10364724-10365539	HUVEC	blood vessel:	n/a	chr12:10364966-10364974 chr12:10365426-10365435 chr12:10364896-10364909 chr12:10365445-10365454 chr12:10365421-10365430
24	POLR2A	chr12:10365273-10365781	HCT-116	colon:	n/a	n/a
25	EGR1	chr12:10364800-10366228	HCT-116	colon:	n/a	chr12:10365422-10365432 chr12:10365421-10365431 chr12:10365012-10365019 chr12:10365864-10365878
26	MAX	chr12:10364688-10365554	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr12:10364785-10367267	MCF10A-Er-Src	breast:	n/a	n/a
28	STAT3	chr12:10364774-10365360	Hela-S3	cervix:	n/a	chr12:10365053-10365065
29	POLR2A	chr12:10364768-10367850	Hela-S3	cervix:	n/a	n/a
30	HCFC1	chr12:10364801-10365578	K562	blood:	n/a	n/a
31	SP1	chr12:10364583-10365868	HCT-116	colon:	n/a	chr12:10365423-10365437 chr12:10365422-10365432 chr12:10365421-10365433 chr12:10365421-10365433 chr12:10365428-10365437 chr12:10365561-10365570 chr12:10365428-10365437 chr12:10365426-10365438 chr12:10365423-10365432 chr12:10365427-10365436 chr12:10365422-10365431 chr12:10365560-10365569 chr12:10365422-10365432 chr12:10365423-10365432 chr12:10365426-10365438 chr12:10365418-10365432 chr12:10365560-10365569
32	CREB1	chr12:10364792-10365870	HepG2	liver:	n/a	chr12:10365443-10365456
33	FOS	chr12:10364719-10365624	MCF10A-Er-Src	breast:	n/a	chr12:10364966-10364974 chr12:10365426-10365435 chr12:10365445-10365454 chr12:10365421-10365430
34	MAX	chr12:10364749-10365870	ECC-1	luminal epithelium:	n/a	chr12:10365656-10365666
35	MYC	chr12:10364778-10365578	K562	blood:	n/a	n/a
36	NFIC	chr12:10364770-10365678	ECC-1	luminal epithelium:	n/a	n/a
37	TAF1	chr12:10364931-10365765	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr12:10364780-10366813	Hela-S3	cervix:	n/a	n/a
39	TEAD4	chr12:10364711-10365719	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr12:10364564-10366597	H1-hESC	embryonic stem cell:	n/a	n/a
41	SMARCB1	chr12:10364547-10366841	Hela-S3	cervix:	n/a	chr12:10364966-10364975 chr12:10366071-10366080
42	POLR2A	chr12:10365232-10365657	K562	blood:	n/a	n/a
43	POLR2A	chr12:10365299-10365788	ECC-1	luminal epithelium:	n/a	n/a
44	ZBTB7A	chr12:10365343-10365500	K562	blood:	n/a	n/a
45	E2F4	chr12:10364731-10365849	MCF10A-Er-Src	breast:	n/a	chr12:10365422-10365431 chr12:10365688-10365698 chr12:10365446-10365455 chr12:10365444-10365453
46	MAFK	chr12:10364786-10365421	K562	blood:	n/a	n/a
47	RFX5	chr12:10364695-10365677	Hela-S3	cervix:	n/a	n/a
48	CEBPD	chr12:10365267-10365480	HepG2	liver:	n/a	n/a
49	MAX	chr12:10364753-10365816	ECC-1	luminal epithelium:	n/a	chr12:10365656-10365666
50	TAF1	chr12:10364650-10366760	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:10365255..10367563-chr12:11322614..11325373,2	K562	blood:
2	chr12:10363710..10369534-chr12:10376619..10381190,6	K562	blood:
3	chr1:154946672..154947579-chr12:10365225..10365920,2	Hela-S3	cervix:
4	chr12:10365073..10366945-chr12:10874439..10876168,2	K562	blood:
5	chr12:10364094..10366158-chr12:10825514..10827785,2	K562	blood:
6	chr12:9913257..9914775-chr12:10363988..10366451,2	K562	blood:
7	chr12:9913275..9915086-chr12:10364378..10366451,2	K562	blood:

Variant related genes	Relation type
GABARAPL1	TF binding region
ENSG00000060138	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000110848	Chromatin interaction
ENSG00000134539	Chromatin interaction
ENSG00000256537	Chromatin interaction
ENSG00000111215	Chromatin interaction
ENSG00000173207	Chromatin interaction
ENSG00000212127	Chromatin interaction
ENSG00000060140	Chromatin interaction
ENSG00000256712	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10772243	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10845069	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845070	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11053625	1.00[CHD][hapmap]
rs11834419	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4326886	0.89[GIH][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4764321	0.98[EUR][1000 genomes]
rs7135302	0.96[EUR][1000 genomes]
rs7136468	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9971656	0.96[EUR][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	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1054811	chr12:10350587-10440005	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 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	chr12:10364000-10367400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr12:10364200-10367600	Active TSS	HSMMtube	muscle
3	chr12:10364400-10366600	Active TSS	A549	lung
4	chr12:10364400-10368200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:10364600-10365400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:10364600-10365600	Active TSS	Brain Germinal Matrix	brain
7	chr12:10364600-10365800	Flanking Active TSS	Dnd41	blood
8	chr12:10364600-10366000	Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr12:10364600-10366000	Active TSS	HepG2	liver
10	chr12:10364600-10366200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:10364600-10366200	Active TSS	Fetal Muscle Leg	muscle
12	chr12:10364600-10366200	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr12:10364600-10366200	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr12:10364600-10366400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:10364600-10366400	Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr12:10364600-10366600	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr12:10364600-10366800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:10364600-10366800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:10364600-10366800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:10364600-10366800	Active TSS	Brain Anterior Caudate	brain
21	chr12:10364600-10366800	Active TSS	Fetal Lung	lung
22	chr12:10364600-10367000	Active TSS	Brain Substantia Nigra	brain
23	chr12:10364600-10367000	Active TSS	Stomach Smooth Muscle	stomach
24	chr12:10364600-10367200	Active TSS	Liver	Liver
25	chr12:10364600-10367200	Active TSS	Rectal Smooth Muscle	rectum
26	chr12:10364600-10367400	Active TSS	H9 Cell Line	embryonic stem cell
27	chr12:10364600-10367400	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr12:10364600-10367400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:10364600-10367400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:10364600-10367400	Active TSS	Brain Cingulate Gyrus	brain
31	chr12:10364600-10367400	Active TSS	Thymus	Thymus
32	chr12:10364600-10367600	Active TSS	H1 Cell Line	embryonic stem cell
33	chr12:10364600-10367600	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr12:10364600-10367600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:10364600-10367600	Active TSS	Brain Angular Gyrus	brain
36	chr12:10364600-10367600	Active TSS	Fetal Brain Female	brain
37	chr12:10364600-10367600	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr12:10364600-10367600	Active TSS	K562	blood
39	chr12:10364600-10367600	Active TSS	Osteobl	bone
40	chr12:10364600-10367800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:10364600-10367800	Active TSS	Colon Smooth Muscle	Colon
42	chr12:10364600-10368000	Active TSS	HSMM	muscle
43	chr12:10364600-10368200	Active TSS	Colonic Mucosa	Colon
44	chr12:10364600-10368400	Active TSS	Fetal Kidney	kidney
45	chr12:10364600-10368800	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr12:10364800-10365400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr12:10364800-10365800	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr12:10364800-10365800	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr12:10364800-10365800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:10364800-10366200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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