Variant report

Variant	rs28545309
Chromosome Location	chr1:215255977-215255978
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	CHD2	chr1:215255939-215256139	H1-hESC	embryonic stem cell:	n/a	n/a
2	TBP	chr1:215255970-215256168	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:215255792-215256454	H1-neurons	neurons:	n/a	n/a
4	MAX	chr1:215255863-215256470	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr1:215255960-215256110	AG04450	lung:	n/a	n/a
6	POLR2A	chr1:215255974-215256034	A549	lung:	n/a	n/a
7	CTCF	chr1:215255940-215256090	HPAF	blood vessel:	n/a	n/a
8	CTCF	chr1:215255920-215256070	HBMEC	blood vessel:	n/a	n/a
9	MYC	chr1:215255976-215255991	MCF-7	breast:	n/a	n/a
10	CTCF	chr1:215255880-215256030	HUVEC	blood vessel:	n/a	n/a
11	EGR1	chr1:215255908-215256357	H1-hESC	embryonic stem cell:	n/a	chr1:215256283-215256297
12	MAX	chr1:215255827-215256412	SK-N-SH	brain:	n/a	n/a
13	RAD21	chr1:215255832-215256522	IMR90	lung:	n/a	chr1:215256125-215256138 chr1:215255923-215255933 chr1:215256326-215256339 chr1:215256488-215256501
14	CTCF	chr1:215255920-215256070	AG04449	skin:	n/a	n/a
15	MXI1	chr1:215255832-215256088	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr1:215255837-215256395	H1-hESC	embryonic stem cell:	n/a	n/a
17	E2F6	chr1:215255790-215256330	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:215255926-215256132	H1-hESC	embryonic stem cell:	n/a	n/a
19	MYC	chr1:215255973-215255994	MCF-7	breast:	n/a	n/a
20	SIN3AK20	chr1:215255694-215257396	MCF-7	breast:	n/a	n/a
21	CTCF	chr1:215255880-215256030	HRE	kidney:	n/a	n/a
22	RAD21	chr1:215255893-215256152	SK-N-SH_RA	brain:	n/a	chr1:215256125-215256138 chr1:215255923-215255933
23	CTBP2	chr1:215255151-215256317	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAZ	chr1:215255617-215257431	IMR90	lung:	n/a	chr1:215256538-215256548 chr1:215256544-215256554
25	RXRA	chr1:215255824-215256073	H1-hESC	embryonic stem cell:	n/a	n/a
26	TAF1	chr1:215255886-215256144	SK-N-SH	brain:	n/a	n/a
27	CTCF	chr1:215255960-215256110	HCFaa	heart:	n/a	n/a
28	CTCF	chr1:215255960-215256110	AG04449	skin:	n/a	n/a
29	CTCF	chr1:215255920-215256070	AG09309	skin:	n/a	n/a
30	SIN3A	chr1:215255806-215256257	H1-hESC	embryonic stem cell:	n/a	n/a
31	MXI1	chr1:215255517-215257345	IMR90	lung:	n/a	n/a
32	CTCF	chr1:215255960-215256110	HPAF	blood vessel:	n/a	n/a
33	ZNF263	chr1:215255885-215256302	HEK293-T-REx	kidney:	n/a	chr1:215256042-215256051 chr1:215256054-215256075 chr1:215255892-215255901
34	MYC	chr1:215255959-215256463	MCF-7	breast:	n/a	n/a
35	REST	chr1:215255587-215257488	H1-neurons	neurons:	n/a	chr1:215256946-215256959 chr1:215257126-215257146 chr1:215257132-215257146
36	CTCF	chr1:215255900-215256050	HFF-Myc	foreskin:	n/a	n/a
37	POLR2A	chr1:215255932-215256325	IMR90	lung:	n/a	n/a
38	CTCF	chr1:215255920-215256070	NHDF-neo	bronchial:	n/a	n/a
39	CTCF	chr1:215255960-215256110	AG09319	gingival:	n/a	n/a
40	ZNF143	chr1:215255857-215256162	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr1:215255621-215256465	ProgFib	skin:	n/a	n/a
42	CTCF	chr1:215255940-215256090	AG09309	skin:	n/a	n/a
43	POLR2A	chr1:215255555-215256408	H1-neurons	neurons:	n/a	n/a
44	POLR2A	chr1:215255676-215256365	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
KCNK2	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10779637	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11120483	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11120486	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12088480	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12092312	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12092515	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12133857	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12136349	0.92[ASN][1000 genomes]
rs28753797	0.81[EUR][1000 genomes]
rs66943143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699778	0.94[ASN][1000 genomes]
rs67098096	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7522445	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528306	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7528988	0.88[ASN][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	esv2754411	chr1:215235605-215281605	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3353761	chr1:215255604-215257627	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215254800-215257400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:215254800-215257400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr1:215254800-215259000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:215254800-215260000	Active TSS	Fetal Brain Female	brain
5	chr1:215255000-215256000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:215255000-215256000	Enhancers	Pancreas	Pancrea
7	chr1:215255000-215256200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
8	chr1:215255000-215256800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
9	chr1:215255000-215257000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
10	chr1:215255000-215257200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
11	chr1:215255000-215257200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr1:215255000-215257400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr1:215255000-215257400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr1:215255000-215258400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:215255200-215256000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
16	chr1:215255200-215256000	Bivalent Enhancer	Fetal Heart	heart
17	chr1:215255200-215256000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
18	chr1:215255200-215256000	Flanking Active TSS	NH-A	brain
19	chr1:215255200-215256200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
20	chr1:215255200-215256800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:215255200-215256800	Active TSS	Brain Anterior Caudate	brain
22	chr1:215255200-215257000	Active TSS	Muscle Satellite Cultured Cells	--
23	chr1:215255200-215257000	Enhancers	Spleen	Spleen
24	chr1:215255200-215257200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:215255200-215257200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr1:215255200-215258600	Active TSS	Fetal Brain Male	brain
27	chr1:215255200-215259000	Active TSS	NHDF-Ad	bronchial
28	chr1:215255400-215256000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
29	chr1:215255400-215256000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
30	chr1:215255400-215256000	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
31	chr1:215255400-215256000	Bivalent Enhancer	Esophagus	oesophagus
32	chr1:215255400-215256000	Flanking Bivalent TSS/Enh	NHEK	skin
33	chr1:215255400-215256200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:215255400-215256200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
35	chr1:215255400-215256600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
36	chr1:215255400-215257000	Active TSS	Gastric	stomach
37	chr1:215255400-215257200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:215255400-215257200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
39	chr1:215255400-215257800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
40	chr1:215255600-215256000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:215255600-215256000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:215255600-215256000	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:215255600-215256000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
44	chr1:215255600-215256200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
45	chr1:215255600-215256200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:215255600-215256200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:215255600-215256200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:215255600-215256200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:215255600-215256200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:215255600-215256200	Bivalent Enhancer	Lung	lung

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