Variant report

Variant	rs12356626
Chromosome Location	chr10:99052421-99052422
allele	A/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	GABPA	chr10:99051745-99052832	MCF-7	breast:	n/a	n/a
2	YY1	chr10:99051832-99052739	HCT-116	colon:	n/a	chr10:99052089-99052103
3	NFYA	chr10:99051783-99052749	K562	blood:	n/a	chr10:99052438-99052451
4	HA-E2F1	chr10:99051668-99052820	MCF-7	breast:	n/a	chr10:99052048-99052055 chr10:99052044-99052055
5	SIX5	chr10:99052406-99052790	K562	blood:	n/a	chr10:99052619-99052628 chr10:99052621-99052630 chr10:99052618-99052632
6	PML	chr10:99051730-99052735	GM12878	blood:	n/a	n/a
7	POLR2A	chr10:99051843-99052490	GM12891	blood:	n/a	n/a
8	NFYB	chr10:99051888-99052735	K562	blood:	n/a	chr10:99052470-99052485 chr10:99052438-99052451 chr10:99052438-99052453
9	BACH1	chr10:99052348-99052837	K562	blood:	n/a	chr10:99052752-99052766
10	TAF1	chr10:99051695-99052738	ECC-1	luminal epithelium:	n/a	n/a
11	NFYA	chr10:99052228-99052666	GM12878	blood:	n/a	chr10:99052438-99052451
12	SIN3AK20	chr10:99051729-99052727	MCF-7	breast:	n/a	n/a
13	MAZ	chr10:99051424-99052864	IMR90	lung:	n/a	chr10:99052755-99052764 chr10:99052578-99052588 chr10:99052423-99052433
14	POLR2A	chr10:99051849-99052690	NB4	blood:	n/a	n/a
15	YY1	chr10:99052254-99052554	HCT-116	colon:	n/a	n/a
16	RCOR1	chr10:99051758-99052734	K562	blood:	n/a	n/a
17	HEY1	chr10:99051852-99052504	HepG2	liver:	n/a	n/a
18	STAT3	chr10:99052177-99052635	MCF10A-Er-Src	breast:	n/a	chr10:99052296-99052307 chr10:99052585-99052597 chr10:99052580-99052592
19	POLR2A	chr10:99051851-99052614	MCF-7	breast:	n/a	n/a
20	POLR2A	chr10:99052103-99052483	GM12891	blood:	n/a	n/a
21	TAF1	chr10:99051876-99052517	K562	blood:	n/a	n/a
22	NFIC	chr10:99051826-99052759	HepG2	liver:	n/a	chr10:99052143-99052160 chr10:99052143-99052159
23	CHD1	chr10:99051640-99052635	GM12878	blood:	n/a	n/a
24	TAF1	chr10:99051866-99052589	GM12878	blood:	n/a	n/a
25	TAF1	chr10:99051861-99052542	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr10:99051814-99052587	H1-neurons	neurons:	n/a	n/a
27	MAFK	chr10:99051896-99052898	K562	blood:	n/a	chr10:99052758-99052769 chr10:99052384-99052399 chr10:99052756-99052765
28	POLR2A	chr10:99051695-99052491	HepG2	liver:	n/a	n/a
29	MYC	chr10:99051725-99052753	K562	blood:	n/a	chr10:99052578-99052588 chr10:99052423-99052433
30	SP1	chr10:99051871-99052727	GM12878	blood:	n/a	chr10:99052584-99052593 chr10:99052420-99052431 chr10:99052577-99052589 chr10:99052584-99052593 chr10:99052421-99052430 chr10:99052583-99052592 chr10:99052422-99052431 chr10:99052421-99052435 chr10:99052577-99052589 chr10:99052420-99052432 chr10:99052599-99052608 chr10:99052420-99052432
31	YY1	chr10:99051895-99052691	HepG2	liver:	n/a	chr10:99052089-99052103
32	PML	chr10:99051872-99052553	MCF-7	breast:	n/a	n/a
33	NFYB	chr10:99051702-99052869	Hela-S3	cervix:	n/a	chr10:99052470-99052485 chr10:99052438-99052451 chr10:99052438-99052453
34	FOXM1	chr10:99052063-99052867	GM12878	blood:	n/a	n/a
35	SIX5	chr10:99052345-99052789	GM12878	blood:	n/a	chr10:99052619-99052628 chr10:99052621-99052630 chr10:99052618-99052632
36	MAX	chr10:99051434-99052674	ECC-1	luminal epithelium:	n/a	chr10:99052578-99052588 chr10:99052423-99052433
37	EP300	chr10:99051790-99052490	T-47D	breast:	n/a	n/a
38	YY1	chr10:99051865-99052621	H1-hESC	embryonic stem cell:	n/a	chr10:99052089-99052103
39	YY1	chr10:99051762-99052774	SK-N-SH_RA	brain:	n/a	chr10:99052089-99052103
40	POLR2A	chr10:99051781-99052629	GM12892	blood:	n/a	n/a
41	YY1	chr10:99051916-99052680	GM12891	blood:	n/a	chr10:99052089-99052103
42	MAFK	chr10:99052181-99052816	HepG2	liver:	n/a	chr10:99052758-99052769 chr10:99052384-99052399 chr10:99052756-99052765
43	EP300	chr10:99051800-99052616	A549	lung:	n/a	n/a
44	HEY1	chr10:99051719-99052533	HepG2	liver:	n/a	n/a
45	POLR2A	chr10:99051791-99052623	HL-60	blood:	n/a	n/a
46	SMC3	chr10:99051627-99052600	Hela-S3	cervix:	n/a	n/a
47	MAX	chr10:99051701-99052672	NB4	blood:	n/a	chr10:99052578-99052588 chr10:99052423-99052433
48	YY1	chr10:99052109-99052552	A549	lung:	n/a	n/a
49	SMARCB1	chr10:99051862-99052509	Hela-S3	cervix:	n/a	n/a
50	YY1	chr10:99052239-99052687	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:99050912..99053751-chr10:99091766..99095025,5	MCF-7	breast:
2	chr10:99049975..99053832-chr10:99093402..99096465,5	K562	blood:
3	chr10:99048545..99053546-chr10:99092341..99096465,6	K562	blood:
4	chr10:99050343..99055587-chr10:99077475..99082102,7	MCF-7	breast:
5	chr10:99051058..99054984-chr10:99078319..99082092,7	MCF-7	breast:
6	chr10:99051863..99052445-chr4:76439211..76440158,2	HCT-116	colon:
7	chr10:99051582..99055310-chr10:99077169..99083058,6	K562	blood:
8	chr10:99051582..99054067-chr10:99077169..99079188,3	K562	blood:
9	chr10:99052282..99052884-chr5:41870193..41871067,2	Hela-S3	cervix:
10	chr10:99051045..99053385-chr10:99092824..99094336,2	MCF-7	breast:
11	chr10:99050735..99053520-chr16:284621..286236,2	MCF-7	breast:
12	chr10:99052064..99052648-chr10:99078773..99079491,2	NB4	blood:

Variant related genes	Relation type
ARHGAP19	TF binding region
ARHGAP19-SLIT1	TF binding region
ENSG00000248668	Chromatin interaction
ENSG00000083720	Chromatin interaction
ENSG00000165879	Chromatin interaction
ENSG00000174796	Chromatin interaction
ENSG00000181274	Chromatin interaction
ENSG00000225850	Chromatin interaction
ENSG00000163743	Chromatin interaction
ENSG00000167930	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10509713	0.93[AMR][1000 genomes]
rs11189064	0.87[AMR][1000 genomes]
rs11189065	0.87[AMR][1000 genomes]
rs11189066	0.87[AMR][1000 genomes]
rs11189067	0.87[AMR][1000 genomes]
rs11189072	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189074	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189076	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189077	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189078	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189080	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189081	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189086	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11189087	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11189090	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189092	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189093	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11189094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189095	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11189096	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11189106	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189107	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189109	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189117	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11189118	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11189125	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11189129	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11189136	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11189140	0.87[AMR][1000 genomes]
rs11189141	0.87[AMR][1000 genomes]
rs11189143	0.87[AMR][1000 genomes]
rs11189145	0.93[AMR][1000 genomes]
rs11189146	0.93[AMR][1000 genomes]
rs11189148	0.93[AMR][1000 genomes]
rs11189149	0.93[AMR][1000 genomes]
rs11189158	0.93[AMR][1000 genomes]
rs11189162	0.87[AMR][1000 genomes]
rs11189166	0.93[AMR][1000 genomes]
rs11189170	0.93[AMR][1000 genomes]
rs12355279	0.93[AMR][1000 genomes]
rs12355311	0.87[AMR][1000 genomes]
rs12355523	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12355526	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12356559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12356648	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12356909	0.87[AMR][1000 genomes]
rs12358104	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12358257	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12358267	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12358452	0.87[AMR][1000 genomes]
rs12358777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12359143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12359467	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12359643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12359654	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12360528	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1414742	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1810982	0.87[AMR][1000 genomes]
rs1970191	0.93[AMR][1000 genomes]
rs1970454	0.93[AMR][1000 genomes]
rs41284270	0.93[AMR][1000 genomes]
rs45527941	0.93[AMR][1000 genomes]
rs7917149	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs884450	0.93[AMR][1000 genomes]
rs9645543	0.87[AMR][1000 genomes]
rs9645559	0.87[AMR][1000 genomes]
rs9645560	0.87[AMR][1000 genomes]
rs9645561	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1041614	chr10:98928281-99083056	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1045553	chr10:98944397-99122203	Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv540750	chr10:98944397-99122203	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv831952	chr10:98998344-99145924	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv895914	chr10:99006083-99131676	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv7507	chr10:99031233-99070690	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv975787	chr10:99048466-99061224	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99050200-99052800	Active TSS	K562	blood
2	chr10:99050800-99052800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr10:99050800-99052800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr10:99050800-99052800	Active TSS	GM12878-XiMat	blood
5	chr10:99051000-99052600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr10:99051000-99052600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr10:99051000-99052600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr10:99051000-99052600	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr10:99051000-99052800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr10:99051000-99052800	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr10:99051000-99052800	Active TSS	HSMM	muscle
12	chr10:99051200-99052600	Active TSS	H1 Cell Line	embryonic stem cell
13	chr10:99051200-99052600	Active TSS	H9 Cell Line	embryonic stem cell
14	chr10:99051200-99052600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr10:99051200-99052600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr10:99051200-99052600	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr10:99051200-99052600	Active TSS	NH-A	brain
18	chr10:99051200-99052800	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr10:99051200-99052800	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr10:99051200-99052800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr10:99051200-99052800	Active TSS	Stomach Smooth Muscle	stomach
22	chr10:99051200-99052800	Active TSS	A549	lung
23	chr10:99051200-99052800	Active TSS	NHDF-Ad	bronchial
24	chr10:99051200-99052800	Active TSS	NHLF	lung
25	chr10:99051400-99052600	Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr10:99051400-99052600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr10:99051400-99052600	Active TSS	Fetal Intestine Small	intestine
28	chr10:99051400-99052600	Active TSS	Fetal Muscle Trunk	muscle
29	chr10:99051400-99052600	Active TSS	Fetal Thymus	thymus
30	chr10:99051400-99052800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr10:99051400-99052800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr10:99051400-99052800	Active TSS	Right Atrium	heart
33	chr10:99051600-99052600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr10:99051600-99052600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr10:99051600-99052600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr10:99051600-99052600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr10:99051600-99052600	Active TSS	Fetal Muscle Leg	muscle
38	chr10:99051600-99052600	Active TSS	Ovary	ovary
39	chr10:99051600-99052800	Active TSS	Brain Hippocampus Middle	brain
40	chr10:99051800-99052600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr10:99051800-99052600	Active TSS	Primary B cells from peripheral blood	blood
42	chr10:99051800-99052600	Active TSS	Primary T cells fromperipheralblood	blood
43	chr10:99051800-99052600	Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr10:99051800-99052600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr10:99051800-99052600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr10:99051800-99052600	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr10:99051800-99052600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr10:99051800-99052600	Active TSS	Liver	Liver
49	chr10:99051800-99052600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
50	chr10:99051800-99052600	Active TSS	Fetal Brain Female	brain

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