Variant report

Variant	rs12031943
Chromosome Location	chr1:227921724-227921725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:227921577-227921851	MCF-7	breast:	n/a	n/a
2	MAX	chr1:227921570-227921975	MCF-7	breast:	n/a	n/a
3	POLR2A	chr1:227921688-227921808	A549	lung:	n/a	n/a
4	RCOR1	chr1:227921672-227921760	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:227921398-227921838	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr1:227921488-227921908	K562	blood:	n/a	n/a
7	MXI1	chr1:227921582-227923837	IMR90	lung:	n/a	n/a
8	MYC	chr1:227921640-227921775	MCF-7	breast:	n/a	n/a
9	POLR2A	chr1:227915700-227921841	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:227920345-227921869	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:227915660-227921896	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:227921504-227921897	MCF-7	breast:	n/a	n/a
13	POLR2A	chr1:227921376-227921914	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:227921425-227921973	HL-60	blood:	n/a	n/a
15	POLR2A	chr1:227916255-227921984	K562	blood:	n/a	n/a
16	POLR2A	chr1:227916827-227921915	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:227916248-227922017	SK-N-MC	brain:	n/a	n/a
18	MYC	chr1:227921655-227921800	MCF-7	breast:	n/a	n/a
19	POLR2A	chr1:227920996-227921895	GM12892	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:227921688-227921738	HCM	heart:	n/a
2	chr1:227921688-227921738	AoSMC	blood vessel:	n/a
3	chr1:227921688-227921738	H1-hESC	embryonic stem cell:	embryo
4	chr1:227921688-227921738	ovcar-3	ovarian:	n/a
5	chr1:227921688-227921738	ECC-1	luminal epithelium:	n/a
6	chr1:227921688-227921738	IMR90	lung:	fetal
7	chr1:227921688-227921738	HUVEC	blood vessel:	n/a
8	chr1:227921688-227921738	SK-N-SH_RA	brain:	n/a
9	chr1:227921688-227921738	NH-A	brain:	n/a
10	chr1:227921688-227921738	GM12892	blood:	n/a
11	chr1:227921688-227921738	HPAEpiC	pulmonary alveolar:	n/a
12	chr1:227921688-227921738	AG10803	skin:	n/a
13	chr1:227921688-227921738	HRCEpiC	kidney:	n/a
14	chr1:227921688-227921738	T-47D	breast:	n/a
15	chr1:227921688-227921738	HCF	heart:	n/a
16	chr1:227921688-227921738	NT2-D1	testis:	n/a
17	chr1:227921688-227921738	HRPEpiC	eye:	n/a
18	chr1:227921688-227921738	HEK293	kidney:	embryo
19	chr1:227921688-227921738	AG09319	gingival:	n/a
20	chr1:227921688-227921738	HNPCEpiC	eye:	n/a
21	chr1:227921688-227921738	Hela-S3	cervix:	n/a
22	chr1:227921688-227921738	Caco-2	colon:	n/a
23	chr1:227921688-227921738	HCT-116	colon:	n/a
24	chr1:227921688-227921738	AG04449	skin:	fetal
25	chr1:227921688-227921738	RPTEC	kidney:	n/a
26	chr1:227921688-227921738	HRE	kidney:	n/a
27	chr1:227921688-227921738	LNCaP	prostate:	n/a
28	chr1:227921688-227921738	Hepatocyte	liver:	n/a
29	chr1:227921688-227921738	SK-N-MC	brain:	n/a
30	chr1:227921688-227921738	HIPEpiC	eye:	n/a
31	chr1:227921688-227921738	MCF-7	breast:	n/a
32	chr1:227921688-227921738	BJ	skin:	n/a
33	chr1:227921688-227921738	HAEpiC	amniotic membrane:	n/a
34	chr1:227921688-227921738	PrEC	prostate:	n/a
35	chr1:227921688-227921738	AG04450	lung:	fetal
36	chr1:227921688-227921738	NB4	blood:	n/a
37	chr1:227921688-227921738	K562	blood:	n/a
38	chr1:227921688-227921738	NHDF-neo	bronchial:	n/a
39	chr1:227921688-227921738	GM12891	blood:	n/a
40	chr1:227921688-227921738	BE2_C	brain:	n/a
41	chr1:227921688-227921738	HCPEpiC	choroid plexus:	n/a
42	chr1:227921688-227921738	PFSK-1	brain:	n/a
43	chr1:227921688-227921738	SK-N-SH	brain:	n/a
44	chr1:227921688-227921738	SKMC	muscle:	n/a
45	chr1:227921688-227921738	HEEpiC	esophagus:	n/a
46	chr1:227921688-227921738	HMEC	breast:	n/a
47	chr1:227921688-227921738	GM06990	blood:	n/a
48	chr1:227921688-227921738	GM19239	blood:	n/a
49	chr1:227921688-227921738	U87	brain:	n/a
50	chr1:227921688-227921738	ProgFib	skin:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227921116..227923050-chr1:228289460..228292114,2	MCF-7	breast:
2	chr1:227918805..227924684-chr1:227929963..227939883,12	K562	blood:
3	chr1:227754198..227755750-chr1:227920040..227921876,2	K562	blood:
4	chr1:227921488..227923041-chr1:228269667..228272192,2	MCF-7	breast:
5	chr1:227916221..227923035-chr1:228131852..228141791,18	MCF-7	breast:

No data

Variant related genes	Relation type
SNAP47	TF binding region
SNAP47	CpG island
ENSG00000143740	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000143816	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000230005	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs10916168	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	esv3387540	chr1:227919379-227922177	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	n/a
9	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 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	chr1:227917000-227921800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:227917000-227921800	Weak transcription	Psoas Muscle	Psoas
3	chr1:227917200-227922000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:227918200-227921800	Genic enhancers	Fetal Muscle Leg	muscle
5	chr1:227918400-227921800	Genic enhancers	Fetal Muscle Trunk	muscle
6	chr1:227918400-227922000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:227918600-227922000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:227918600-227922000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:227918800-227921800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:227919000-227921800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:227919000-227922000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:227919200-227921800	Strong transcription	Fetal Intestine Small	intestine
13	chr1:227919400-227921800	Genic enhancers	Liver	Liver
14	chr1:227920400-227921800	Transcr. at gene 5' and 3'	Spleen	Spleen
15	chr1:227920400-227922000	Genic enhancers	Right Ventricle	heart
16	chr1:227920600-227921800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:227920600-227921800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr1:227920600-227921800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
19	chr1:227920600-227922000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:227920800-227922000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:227920800-227922000	Genic enhancers	Gastric	stomach
22	chr1:227921000-227921800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr1:227921000-227921800	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:227921000-227921800	Genic enhancers	Adipose Nuclei	Adipose
25	chr1:227921000-227922000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:227921200-227921800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:227921200-227921800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:227921200-227921800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
29	chr1:227921200-227921800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:227921200-227921800	Genic enhancers	Placenta	Placenta
31	chr1:227921200-227921800	Genic enhancers	Fetal Stomach	stomach
32	chr1:227921200-227921800	Genic enhancers	Ovary	ovary
33	chr1:227921200-227921800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
34	chr1:227921200-227921800	Transcr. at gene 5' and 3'	Dnd41	blood
35	chr1:227921200-227922000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:227921200-227922000	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:227921200-227922000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr1:227921200-227922000	Enhancers	Brain Angular Gyrus	brain
39	chr1:227921200-227922200	Enhancers	Primary B cells from peripheral blood	blood
40	chr1:227921200-227922200	Weak transcription	Aorta	Aorta
41	chr1:227921400-227921800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:227921400-227921800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:227921400-227921800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:227921400-227921800	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
45	chr1:227921400-227921800	Enhancers	HSMMtube	muscle
46	chr1:227921400-227921800	Enhancers	NH-A	brain
47	chr1:227921400-227922000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:227921400-227922000	Enhancers	Primary B cells from cord blood	blood
49	chr1:227921400-227922000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr1:227921400-227922000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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