Variant report

Variant	rs12193627
Chromosome Location	chr6:146057289-146057290
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	NR2F2	chr6:146056694-146057290	K562	blood:	n/a	n/a
2	CREB1	chr6:146055654-146057365	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:146055017-146057985	GM12878	blood:	n/a	n/a
4	MAZ	chr6:146055828-146057530	GM12878	blood:	n/a	chr6:146056754-146056763 chr6:146057245-146057254 chr6:146056754-146056761 chr6:146056752-146056765
5	E2F4	chr6:146057213-146057371	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr6:146055648-146057475	GM18505	blood:	n/a	n/a
7	TBL1XR1	chr6:146056847-146057323	K562	blood:	n/a	n/a
8	RELA	chr6:146055855-146057366	GM18505	blood:	n/a	n/a
9	BCLAF1	chr6:146055626-146057292	K562	blood:	n/a	chr6:146056929-146056938 chr6:146056638-146056651 chr6:146056681-146056694 chr6:146055898-146055911 chr6:146056643-146056652 chr6:146056085-146056098 chr6:146056635-146056648 chr6:146056640-146056649
10	SMC3	chr6:146056670-146057397	GM12878	blood:	n/a	n/a
11	TBP	chr6:146056796-146057441	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr6:146055475-146057511	H1-hESC	embryonic stem cell:	n/a	n/a
13	HEY1	chr6:146055696-146057362	K562	blood:	n/a	chr6:146056637-146056652 chr6:146055900-146055915 chr6:146056231-146056246 chr6:146056237-146056252
14	POLR2A	chr6:146055656-146057448	GM12892	blood:	n/a	n/a
15	POLR2A	chr6:146056595-146057319	U87	brain:	n/a	n/a
16	MTA3	chr6:146056447-146057491	GM12878	blood:	n/a	n/a
17	MTA3	chr6:146056565-146057445	GM12878	blood:	n/a	n/a
18	E2F4	chr6:146055786-146057293	K562	blood:	n/a	chr6:146056134-146056143 chr6:146056078-146056090 chr6:146056683-146056693 chr6:146056820-146056832 chr6:146056229-146056238 chr6:146056640-146056650 chr6:146056008-146056017 chr6:146056237-146056247 chr6:146056246-146056256
19	POLR2A	chr6:146055775-146057355	MCF-7	breast:	n/a	n/a
20	NFYA	chr6:146057098-146057399	K562	blood:	n/a	chr6:146057213-146057227 chr6:146057215-146057225 chr6:146057212-146057227 chr6:146057212-146057227
21	POLR2A	chr6:146055717-146057378	Raji	blood:	n/a	n/a
22	FOXM1	chr6:146056885-146057476	GM12878	blood:	n/a	n/a
23	USF2	chr6:146056240-146057314	GM12878	blood:	n/a	chr6:146056676-146056692
24	POLR2A	chr6:146055638-146057308	K562	blood:	n/a	n/a
25	POLR2A	chr6:146055853-146057312	GM12891	blood:	n/a	n/a
26	RELA	chr6:146056030-146057423	GM19099	blood:	n/a	n/a
27	POLR2A	chr6:146055715-146057383	GM12892	blood:	n/a	n/a
28	CEBPB	chr6:146056880-146057388	K562	blood:	n/a	n/a
29	TBP	chr6:146055695-146057363	HepG2	liver:	n/a	n/a
30	RELA	chr6:146055679-146057320	GM15510	blood:	n/a	n/a
31	MYBL2	chr6:146056608-146057384	HepG2	liver:	n/a	n/a
32	RELA	chr6:146056026-146057389	GM18951	blood:	n/a	n/a
33	ELF1	chr6:146055798-146057366	GM12878	blood:	n/a	chr6:146056131-146056140 chr6:146056232-146056241 chr6:146056639-146056648 chr6:146056642-146056651 chr6:146056737-146056749
34	POLR2A	chr6:146055407-146057502	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr6:146055702-146057321	K562	blood:	n/a	n/a
36	STAT5A	chr6:146056768-146057304	GM12878	blood:	n/a	chr6:146056952-146056960
37	YY1	chr6:146055701-146057317	GM12878	blood:	n/a	chr6:146056242-146056256 chr6:146056642-146056651 chr6:146056640-146056651 chr6:146056304-146056318 chr6:146056680-146056694 chr6:146055903-146055914 chr6:146056239-146056253 chr6:146056310-146056321 chr6:146056639-146056653 chr6:146056639-146056648 chr6:146056672-146056681 chr6:146056636-146056650
38	TAF1	chr6:146056665-146057332	H1-neurons	neurons:	n/a	n/a
39	MXI1	chr6:146054723-146057920	SK-N-SH	brain:	n/a	n/a
40	TAF1	chr6:146055794-146057359	GM12878	blood:	n/a	n/a
41	MAFF	chr6:146057010-146058120	K562	blood:	n/a	chr6:146057511-146057529
42	POLR2A	chr6:146055662-146057437	PFSK-1	brain:	n/a	n/a
43	POLR2A	chr6:146055598-146057359	Hela-S3	cervix:	n/a	n/a
44	USF2	chr6:146056640-146057376	Hela-S3	cervix:	n/a	chr6:146056676-146056692
45	PML	chr6:146055539-146057424	K562	blood:	n/a	n/a
46	ZNF143	chr6:146055698-146057318	GM12878	blood:	n/a	chr6:146056636-146056646
47	IKZF1	chr6:146056843-146057411	GM12878	blood:	n/a	n/a
48	GTF2F1	chr6:146055826-146057329	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr6:146055750-146058001	GM19099	blood:	n/a	n/a
50	MAFK	chr6:146056895-146058034	K562	blood:	n/a	chr6:146057517-146057528 chr6:146057515-146057529 chr6:146057512-146057527 chr6:146057516-146057527 chr6:146057517-146057528 chr6:146057512-146057528

No.	Distal block	Cell Line	Cell type
1	chr6:43595203..43596723-chr6:146055866..146057723,2	MCF-7	breast:
2	chr6:146055478..146057329-chr6:146213622..146216410,2	K562	blood:
3	chr6:146054764..146058281-chr6:146133205..146137397,13	MCF-7	breast:
4	chr6:146054881..146058754-chr6:146284576..146286666,3	K562	blood:
5	chr19:55770065..55771348-chr6:146056333..146057332,3	Hela-S3	cervix:
6	chr6:146055814..146058166-chr6:146135376..146138309,3	MCF-7	breast:
7	chr6:146051601..146058492-chr6:146282422..146286666,8	K562	blood:
8	chr1:110950353..110950869-chr6:146056622..146057613,2	Hela-S3	cervix:
9	chr6:146052168..146062191-chr6:146124046..146141258,59	K562	blood:
10	chr6:146047378..146061811-chr6:146118130..146137627,77	K562	blood:
11	chr6:146054743..146057884-chr6:146276241..146279001,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRM1-11	chr6:146056706-146058354	ENSG00000270638.1

Variant related genes	Relation type
EPM2A	TF binding region
ENSG00000118496	Chromatin interaction
ENSG00000134248	Chromatin interaction
ENSG00000235652	Chromatin interaction
ENSG00000224699	Chromatin interaction
ENSG00000172432	Chromatin interaction
ENSG00000146414	Chromatin interaction
ENSG00000105063	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10457055	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12195117	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12195987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198683	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12200607	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12203609	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12205454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12212636	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12214705	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13196875	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13200495	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13201738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13203662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13210966	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28703599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34211445	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34312543	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35587488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35667536	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35807318	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6899772	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73579446	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9485004	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs952407	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]

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	esv3424432	chr6:146041308-146057603	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv3471925	chr6:146054784-146057832	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv3471926	chr6:146054784-146057832	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv3384876	chr6:146055559-146057657	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146054800-146057800	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr6:146054800-146058400	Active TSS	Stomach Smooth Muscle	stomach
3	chr6:146055000-146057400	Active TSS	Right Ventricle	heart
4	chr6:146055000-146057600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:146055000-146057600	Active TSS	Colon Smooth Muscle	Colon
6	chr6:146055000-146057800	Active TSS	Brain Angular Gyrus	brain
7	chr6:146055000-146058000	Active TSS	Fetal Stomach	stomach
8	chr6:146055000-146058000	Active TSS	Thymus	Thymus
9	chr6:146055000-146058400	Active TSS	Brain Germinal Matrix	brain
10	chr6:146055000-146058400	Active TSS	Right Atrium	heart
11	chr6:146055200-146057400	Active TSS	H1 Cell Line	embryonic stem cell
12	chr6:146055200-146057400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:146055200-146057400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:146055200-146057400	Active TSS	Fetal Thymus	thymus
15	chr6:146055200-146057400	Active TSS	Psoas Muscle	Psoas
16	chr6:146055200-146057400	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr6:146055200-146057600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:146055200-146058000	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr6:146055200-146058000	Active TSS	Fetal Muscle Leg	muscle
20	chr6:146055200-146058400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:146055400-146057400	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr6:146055400-146057400	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr6:146055400-146057400	Active TSS	Primary T killer memory cells from peripheral blood	blood
24	chr6:146055400-146057400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr6:146055400-146057400	Active TSS	Fetal Intestine Small	intestine
26	chr6:146055400-146057400	Active TSS	Fetal Kidney	kidney
27	chr6:146055400-146057400	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr6:146055400-146057600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:146055400-146057600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:146055400-146057600	Active TSS	Fetal Intestine Large	intestine
31	chr6:146055400-146057600	Active TSS	Fetal Lung	lung
32	chr6:146055400-146057800	Active TSS	Rectal Smooth Muscle	rectum
33	chr6:146055400-146058000	Active TSS	Rectal Mucosa Donor 31	rectum
34	chr6:146055400-146058000	Active TSS	GM12878-XiMat	blood
35	chr6:146055400-146058400	Active TSS	Brain Anterior Caudate	brain
36	chr6:146055600-146057400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr6:146055600-146057400	Active TSS	H9 Cell Line	embryonic stem cell
38	chr6:146055600-146057400	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr6:146055600-146057400	Active TSS	Primary T cells fromperipheralblood	blood
40	chr6:146055600-146057400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:146055600-146057400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:146055600-146057400	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr6:146055600-146057400	Active TSS	Colonic Mucosa	Colon
44	chr6:146055600-146057400	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr6:146055600-146057400	Active TSS	Fetal Muscle Trunk	muscle
46	chr6:146055600-146057400	Active TSS	A549	lung
47	chr6:146055600-146057400	Active TSS	Hela-S3	cervix
48	chr6:146055600-146057600	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr6:146055600-146057600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:146055600-146057600	Active TSS	Primary T cells from cord blood	blood

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