Variant report

Variant	rs1677075
Chromosome Location	chr12:21809641-21809642
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	BCL3	chr12:21809563-21811078	A549	lung:	n/a	chr12:21810566-21810575 chr12:21810400-21810409 chr12:21810534-21810547
2	POLR2A	chr12:21809612-21811117	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD1	chr12:21808698-21810976	H1-hESC	embryonic stem cell:	n/a	chr12:21809894-21809904
4	SIN3A	chr12:21809620-21810996	GM12878	blood:	n/a	chr12:21810400-21810410
5	POLR2A	chr12:21809471-21811125	GM12878	blood:	n/a	n/a
6	MYC	chr12:21809513-21810961	MCF10A-Er-Src	breast:	n/a	chr12:21810341-21810352 chr12:21810784-21810794 chr12:21810919-21810929 chr12:21810137-21810146 chr12:21810781-21810791
7	MYC	chr12:21809323-21811088	MCF10A-Er-Src	breast:	n/a	chr12:21810341-21810352 chr12:21810784-21810794 chr12:21810919-21810929 chr12:21810137-21810146 chr12:21810781-21810791
8	POLR2A	chr12:21809282-21811114	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr12:21808471-21811183	GM12891	blood:	n/a	n/a
10	POLR2A	chr12:21808476-21811157	MCF10A-Er-Src	breast:	n/a	n/a
11	SIN3A	chr12:21809462-21811156	H1-hESC	embryonic stem cell:	n/a	chr12:21810400-21810410
12	REST	chr12:21809379-21811195	H1-neurons	neurons:	n/a	chr12:21810192-21810200 chr12:21810322-21810335 chr12:21810400-21810409 chr12:21809930-21809948
13	REST	chr12:21809632-21811200	A549	lung:	n/a	chr12:21810192-21810200 chr12:21810322-21810335 chr12:21810400-21810409 chr12:21809930-21809948
14	PML	chr12:21809640-21811223	GM12878	blood:	n/a	chr12:21810691-21810699
15	MAX	chr12:21809122-21811140	NB4	blood:	n/a	chr12:21810341-21810352 chr12:21810784-21810794 chr12:21810919-21810929 chr12:21810137-21810146 chr12:21810781-21810791
16	POLR2A	chr12:21809591-21811099	GM12878	blood:	n/a	n/a
17	MYC	chr12:21809126-21811134	NB4	blood:	n/a	chr12:21810341-21810352 chr12:21810784-21810794 chr12:21810919-21810929 chr12:21810137-21810146 chr12:21810781-21810791
18	POLR2A	chr12:21807938-21811135	K562	blood:	n/a	n/a
19	POLR2A	chr12:21808265-21811279	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr12:21809053-21811207	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr12:21809553-21811159	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr12:21808688-21810981	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr12:21809590-21811138	MCF10A-Er-Src	breast:	n/a	n/a
24	MXI1	chr12:21809225-21811200	IMR90	lung:	n/a	n/a
25	MXI1	chr12:21808325-21811442	SK-N-SH	brain:	n/a	n/a
26	TCF12	chr12:21809498-21811306	A549	lung:	n/a	n/a
27	IRF1	chr12:21808446-21811074	K562	blood:	n/a	chr12:21808676-21808690 chr12:21809480-21809494 chr12:21808675-21808688 chr12:21809874-21809886 chr12:21808677-21808688 chr12:21809874-21809886 chr12:21809477-21809494 chr12:21808675-21808688 chr12:21809480-21809491 chr12:21808679-21808689 chr12:21809478-21809491 chr12:21808676-21808688 chr12:21808673-21808687 chr12:21808670-21808684 chr12:21810785-21810799 chr12:21808675-21808688 chr12:21809479-21809496 chr12:21808674-21808688 chr12:21808676-21808689 chr12:21808671-21808682 chr12:21808676-21808690 chr12:21809230-21809247 chr12:21808669-21808689 chr12:21808676-21808688 chr12:21808675-21808688 chr12:21809480-21809490 chr12:21809874-21809885 chr12:21809869-21809886 chr12:21809476-21809490
28	MAX	chr12:21809481-21811155	A549	lung:	n/a	chr12:21810341-21810352 chr12:21810784-21810794 chr12:21810919-21810929 chr12:21810137-21810146 chr12:21810781-21810791

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:21589456..21592020-chr12:21808889..21812230,4	K562	blood:
2	chr12:21809057..21812387-chr12:22198017..22201408,5	K562	blood:

Variant related genes	Relation type
LDHB	TF binding region
ENSG00000121350	Chromatin interaction
ENSG00000111726	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11836605	1.00[AMR][1000 genomes]
rs1283818	1.00[AMR][1000 genomes]
rs153942	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1650272	1.00[AMR][1000 genomes]
rs1650311	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1677080	0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1677081	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1677090	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs1677124	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs1677129	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs1677134	0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1677140	1.00[AMR][1000 genomes]
rs255450	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs255454	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60507695	1.00[AMR][1000 genomes]
rs60867568	1.00[AMR][1000 genomes]
rs61320912	1.00[AMR][1000 genomes]
rs704199	1.00[AMR][1000 genomes]
rs704200	1.00[AMR][1000 genomes]
rs704201	1.00[AMR][1000 genomes]
rs73249205	1.00[AMR][1000 genomes]
rs73258133	1.00[AMR][1000 genomes]
rs73260142	1.00[AMR][1000 genomes]
rs73260149	1.00[AMR][1000 genomes]
rs73262354	1.00[AMR][1000 genomes]
rs73262383	1.00[AMR][1000 genomes]
rs73262391	1.00[AMR][1000 genomes]
rs73262395	1.00[AMR][1000 genomes]
rs73266378	1.00[AMR][1000 genomes]
rs73266381	1.00[AMR][1000 genomes]
rs759933	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs829071	1.00[AMR][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	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv469164	chr12:21688900-21966701	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv557744	chr12:21688900-21966701	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv832349	chr12:21749093-21930695	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21788600-21810000	Weak transcription	Liver	Liver
2	chr12:21804200-21810000	Weak transcription	Stomach Mucosa	stomach
3	chr12:21804400-21810000	Weak transcription	Spleen	Spleen
4	chr12:21804600-21809800	Weak transcription	Esophagus	oesophagus
5	chr12:21804600-21809800	Weak transcription	Gastric	stomach
6	chr12:21806000-21810600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
7	chr12:21807000-21809800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
8	chr12:21807000-21810200	Transcr. at gene 5' and 3'	A549	lung
9	chr12:21807400-21809800	Weak transcription	Colonic Mucosa	Colon
10	chr12:21807600-21809800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:21807600-21811400	Active TSS	GM12878-XiMat	blood
12	chr12:21807800-21810200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr12:21808000-21810200	Active TSS	Right Atrium	heart
14	chr12:21808200-21809800	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr12:21808200-21810800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:21808200-21811000	Active TSS	Primary T cells fromperipheralblood	blood
17	chr12:21808200-21811200	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr12:21808200-21811200	Active TSS	K562	blood
19	chr12:21808400-21809800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:21808400-21810600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:21808400-21811200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:21808400-21811200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:21808600-21810800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:21808600-21810800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:21808600-21810800	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr12:21808600-21810800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:21808600-21811200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:21808600-21811200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr12:21808600-21811200	Active TSS	Brain Substantia Nigra	brain
30	chr12:21808600-21811200	Active TSS	Ovary	ovary
31	chr12:21808600-21811200	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr12:21808600-21811200	Active TSS	Right Ventricle	heart
33	chr12:21808600-21811400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:21808600-21811800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:21808800-21809800	Flanking Active TSS	HUVEC	blood vessel
36	chr12:21808800-21811200	Active TSS	H1 Cell Line	embryonic stem cell
37	chr12:21808800-21811200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:21808800-21811200	Active TSS	Psoas Muscle	Psoas
39	chr12:21808800-21811600	Active TSS	Fetal Kidney	kidney
40	chr12:21809000-21809800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr12:21809000-21809800	Flanking Active TSS	Hela-S3	cervix
42	chr12:21809000-21810400	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr12:21809000-21810400	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr12:21809000-21810800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:21809000-21810800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:21809000-21811200	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr12:21809000-21811200	Active TSS	H9 Cell Line	embryonic stem cell
48	chr12:21809000-21811200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:21809000-21811200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr12:21809000-21811200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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