Variant report

Variant	rs28695935
Chromosome Location	chr12:121974375-121974376
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	ESR1	chr12:121973988-121974831	ECC-1	luminal epithelium:	n/a	n/a
2	MXI1	chr12:121973624-121976489	SK-N-SH	brain:	n/a	n/a
3	SP1	chr12:121973983-121974728	GM12878	blood:	n/a	chr12:121974660-121974672 chr12:121974474-121974483 chr12:121974660-121974672 chr12:121974473-121974483 chr12:121974080-121974094 chr12:121974079-121974091 chr12:121974662-121974671
4	CHD2	chr12:121974366-121974539	K562	blood:	n/a	n/a
5	RUNX3	chr12:121973725-121975930	GM12878	blood:	n/a	n/a
6	ELK1	chr12:121973952-121974609	GM12878	blood:	n/a	n/a
7	SIN3AK20	chr12:121974016-121974403	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr12:121972301-121975787	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:121973933-121974451	GM12891	blood:	n/a	n/a
10	RFX5	chr12:121974001-121974813	GM12878	blood:	n/a	chr12:121974251-121974260 chr12:121974249-121974263 chr12:121974247-121974261
11	EBF1	chr12:121974358-121975769	GM12878	blood:	n/a	n/a
12	SMARCB1	chr12:121973841-121976449	Hela-S3	cervix:	n/a	n/a
13	ELF1	chr12:121973969-121975832	GM12878	blood:	n/a	chr12:121975821-121975830 chr12:121975526-121975538 chr12:121975106-121975118 chr12:121975222-121975233
14	EBF1	chr12:121973606-121974451	GM12878	blood:	n/a	n/a
15	MAX	chr12:121974000-121974757	K562	blood:	n/a	chr12:121974080-121974090
16	POLR2A	chr12:121973583-121974512	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:121974302-121974381	ProgFib	skin:	n/a	n/a
18	EP300	chr12:121974316-121974548	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:121973892-121974493	GM12878	blood:	n/a	n/a
20	MAZ	chr12:121973926-121975373	K562	blood:	n/a	chr12:121975043-121975053 chr12:121974080-121974090
21	NFYB	chr12:121973973-121974439	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:121973547-121975876	GM12892	blood:	n/a	n/a
23	POLR2A	chr12:121973653-121976782	GM19193	blood:	n/a	n/a
24	POLR2A	chr12:121974007-121974467	ECC-1	luminal epithelium:	n/a	n/a
25	E2F6	chr12:121974169-121974406	K562	blood:	n/a	n/a
26	RELA	chr12:121973849-121975728	GM19193	blood:	n/a	n/a
27	POLR2A	chr12:121973609-121976415	GM18951	blood:	n/a	n/a
28	FOXM1	chr12:121973936-121975631	GM12878	blood:	n/a	n/a
29	RFX5	chr12:121974124-121974380	H1-hESC	embryonic stem cell:	n/a	chr12:121974251-121974260 chr12:121974249-121974263 chr12:121974247-121974261
30	NFATC1	chr12:121974248-121974998	GM12878	blood:	n/a	n/a
31	MAZ	chr12:121973768-121976444	GM12878	blood:	n/a	chr12:121975043-121975053 chr12:121974080-121974090 chr12:121976078-121976088
32	CUX1	chr12:121974331-121974737	GM12878	blood:	n/a	n/a
33	ZNF384	chr12:121974141-121974794	K562	blood:	n/a	n/a
34	POLR2A	chr12:121973761-121976612	GM12892	blood:	n/a	n/a
35	POLR2A	chr12:121974256-121974398	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr12:121973771-121974820	H1-neurons	neurons:	n/a	n/a
37	MAX	chr12:121973713-121977024	ECC-1	luminal epithelium:	n/a	chr12:121975043-121975053 chr12:121975245-121975255 chr12:121974080-121974090 chr12:121976078-121976088 chr12:121973741-121973751
38	EP300	chr12:121974161-121974681	GM12878	blood:	n/a	n/a
39	NFIC	chr12:121974016-121974741	GM12878	blood:	n/a	n/a
40	NFATC1	chr12:121974229-121974860	GM12878	blood:	n/a	n/a
41	NFIC	chr12:121974305-121975827	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr12:121973946-121975930	SK-N-MC	brain:	n/a	n/a
43	CTBP2	chr12:121973869-121974694	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr12:121973711-121976427	GM12892	blood:	n/a	n/a
45	POLR2A	chr12:121973296-121976832	GM12878	blood:	n/a	n/a
46	POU2F2	chr12:121973522-121975432	GM12891	blood:	n/a	chr12:121973579-121973591 chr12:121975131-121975143
47	RELA	chr12:121974144-121975706	GM10847	blood:	n/a	n/a
48	RCOR1	chr12:121973996-121974422	K562	blood:	n/a	n/a
49	REST	chr12:121973568-121976423	H1-neurons	neurons:	n/a	chr12:121973990-121974003 chr12:121975043-121975056 chr12:121976004-121976014 chr12:121974811-121974821 chr12:121974313-121974333
50	CREB1	chr12:121973803-121975810	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:121973453..121977492-chr12:122016919..122020388,4	K562	blood:
2	chr12:121966142..121973158-chr12:121973289..121976781,9	MCF-7	breast:
3	chr12:121973525..121977245-chr12:122063799..122066216,4	K562	blood:
4	chr12:121972742..121976523-chr12:121985100..121990052,4	K562	blood:
5	chr12:121973342..121977941-chr12:121987524..121992877,7	MCF-7	breast:

Variant related genes	Relation type
KDM2B	TF binding region
ENSG00000182500	Chromatin interaction
ENSG00000256742	Chromatin interaction
ENSG00000089094	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11065533	1.00[EUR][1000 genomes]
rs12305100	1.00[EUR][1000 genomes]
rs12305609	1.00[EUR][1000 genomes]
rs12313456	1.00[EUR][1000 genomes]
rs28637307	1.00[EUR][1000 genomes]
rs7135308	1.00[EUR][1000 genomes]
rs7957459	1.00[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	nsv560457	chr12:121956483-121976176	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
4	esv3354947	chr12:121974194-121976742	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121932000-121974400	Weak transcription	NHEK	skin
2	chr12:121968200-121974600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:121969200-121974600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:121971600-121974600	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr12:121971600-121974600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:121972000-121974400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:121972000-121974600	Enhancers	Primary T cells fromperipheralblood	blood
8	chr12:121972200-121974600	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr12:121972200-121974600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:121972200-121974600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr12:121972400-121974600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:121972400-121975000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:121972400-121975200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr12:121972600-121974800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:121972600-121974800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:121972800-121974400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:121972800-121974400	Enhancers	Fetal Heart	heart
18	chr12:121972800-121974600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr12:121973000-121974800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr12:121973200-121974400	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:121973200-121974800	Enhancers	Thymus	Thymus
22	chr12:121973200-121975000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:121973200-121975000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr12:121973200-121976800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr12:121973400-121974800	Flanking Active TSS	Brain Germinal Matrix	brain
26	chr12:121973400-121975200	Active TSS	Fetal Kidney	kidney
27	chr12:121973400-121975200	Flanking Active TSS	Fetal Muscle Trunk	muscle
28	chr12:121973400-121976800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:121973600-121974400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:121973600-121974400	Flanking Active TSS	Brain Angular Gyrus	brain
31	chr12:121973600-121974400	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr12:121973600-121974400	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr12:121973600-121974400	Enhancers	HepG2	liver
34	chr12:121973600-121974600	Enhancers	Primary hematopoietic stem cells	blood
35	chr12:121973600-121974600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:121973600-121974600	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr12:121973600-121974800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr12:121973600-121974800	Flanking Active TSS	Fetal Thymus	thymus
39	chr12:121973600-121975000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:121973600-121975000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:121973600-121975000	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr12:121973600-121975000	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr12:121973600-121975000	Flanking Active TSS	Fetal Intestine Large	intestine
44	chr12:121973600-121975000	Flanking Active TSS	Fetal Intestine Small	intestine
45	chr12:121973600-121975000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr12:121973600-121975000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr12:121973600-121975200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr12:121973600-121975200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr12:121973600-121975200	Flanking Active TSS	Liver	Liver
50	chr12:121973600-121975600	Flanking Active TSS	Fetal Muscle Leg	muscle

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