Variant report

Variant	rs12472454
Chromosome Location	chr2:38979627-38979628
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr2:38977326-38979642	K562	blood:	n/a	chr2:38977600-38977609 chr2:38979316-38979323 chr2:38978721-38978731 chr2:38979315-38979326 chr2:38978724-38978734
2	REST	chr2:38977226-38979675	H1-neurons	neurons:	n/a	chr2:38977794-38977804 chr2:38978974-38978983 chr2:38978212-38978222 chr2:38978584-38978592 chr2:38979114-38979134
3	MXI1	chr2:38973236-38979955	SK-N-SH	brain:	n/a	chr2:38978665-38978680
4	POLR2A	chr2:38967761-38979649	H1-hESC	embryonic stem cell:	n/a	n/a
5	NFYA	chr2:38979466-38979635	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:38979602-38979652	GM06990	blood:	n/a
2	chr2:38979602-38979652	PFSK-1	brain:	n/a
3	chr2:38979602-38979652	IMR90	lung:	fetal
4	chr2:38979602-38979652	T-47D	breast:	n/a
5	chr2:38979602-38979652	GM12891	blood:	n/a
6	chr2:38979602-38979652	AG09319	gingival:	n/a
7	chr2:38979602-38979652	Hela-S3	cervix:	n/a
8	chr2:38979602-38979652	HEEpiC	esophagus:	n/a
9	chr2:38979602-38979652	SKMC	muscle:	n/a
10	chr2:38979602-38979652	HCT-116	colon:	n/a
11	chr2:38979602-38979652	HUVEC	blood vessel:	n/a
12	chr2:38979602-38979652	NHBE	bronchial:	n/a
13	chr2:38979602-38979652	GM12878	blood:	n/a
14	chr2:38979602-38979652	HL-60	blood:	n/a
15	chr2:38979602-38979652	HMEC	breast:	n/a
16	chr2:38979602-38979652	SK-N-SH	brain:	n/a
17	chr2:38979602-38979652	H1-hESC	embryonic stem cell:	embryo
18	chr2:38979602-38979652	A549	lung:	n/a
19	chr2:38979602-38979652	K562	blood:	n/a
20	chr2:38979602-38979652	HEK293	kidney:	embryo
21	chr2:38979602-38979652	ovcar-3	ovarian:	n/a
22	chr2:38979602-38979652	SK-N-SH_RA	brain:	n/a
23	chr2:38979602-38979652	PANC-1	pancreas:	n/a
24	chr2:38979602-38979652	HPAEpiC	pulmonary alveolar:	n/a
25	chr2:38979602-38979652	MCF-7	breast:	n/a
26	chr2:38979602-38979652	HAEpiC	amniotic membrane:	n/a
27	chr2:38979602-38979652	GM12892	blood:	n/a
28	chr2:38979602-38979652	HRPEpiC	eye:	n/a
29	chr2:38979602-38979652	LNCaP	prostate:	n/a
30	chr2:38979602-38979652	PrEC	prostate:	n/a
31	chr2:38979602-38979652	AG09309	skin:	n/a
32	chr2:38979602-38979652	HRCEpiC	kidney:	n/a
33	chr2:38979602-38979652	SK-N-MC	brain:	n/a
34	chr2:38979602-38979652	NT2-D1	testis:	n/a
35	chr2:38979602-38979652	SAEC	small airway:	n/a
36	chr2:38979602-38979652	Jurkat	blood:	n/a
37	chr2:38979602-38979652	BJ	skin:	n/a
38	chr2:38979602-38979652	CMK	blood:	n/a
39	chr2:38979602-38979652	Hepatocyte	liver:	n/a
40	chr2:38979602-38979652	HCPEpiC	choroid plexus:	n/a
41	chr2:38979602-38979652	HNPCEpiC	eye:	n/a
42	chr2:38979602-38979652	AG10803	skin:	n/a
43	chr2:38979602-38979652	AG04450	lung:	fetal
44	chr2:38979602-38979652	AoSMC	blood vessel:	n/a
45	chr2:38979602-38979652	GM19239	blood:	n/a
46	chr2:38979602-38979652	NH-A	brain:	n/a
47	chr2:38979602-38979652	U87	brain:	n/a
48	chr2:38979602-38979652	RPTEC	kidney:	n/a
49	chr2:38979602-38979652	HCM	heart:	n/a
50	chr2:38979602-38979652	BE2_C	brain:	n/a

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38977870..38980067-chr2:42586942..42589703,3	K562	blood:
2	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
3	chr2:38976936..38979845-chr2:39101241..39105632,7	K562	blood:
4	chr2:38816358..38820230-chr2:38976960..38979820,4	MCF-7	breast:
5	chr2:38976877..38979785-chr2:39100480..39105632,13	K562	blood:
6	chr2:38976218..38980921-chr2:39003670..39007764,15	K562	blood:
7	chr2:37457826..37459742-chr2:38976926..38979723,2	K562	blood:
8	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
9	chr2:38762042..38765801-chr2:38976684..38979922,4	MCF-7	breast:
10	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
11	chr2:38978307..38979883-chr20:23342389..23345213,2	MCF-7	breast:
12	chr2:38828577..38831705-chr2:38976861..38979916,6	MCF-7	breast:
13	chr2:38891861..38895889-chr2:38976029..38979857,7	K562	blood:
14	chr2:38975148..38982473-chr2:39000165..39007764,21	K562	blood:
15	chr2:38879772..38882593-chr2:38978947..38981476,2	K562	blood:
16	chr2:38974221..38979921-chr2:38986851..38994572,21	K562	blood:
17	chr2:38974982..38979904-chr2:39002191..39014206,31	MCF-7	breast:
18	chr2:38977122..38981176-chr2:38994666..38999219,6	K562	blood:
19	chr2:38977033..38979904-chr2:47402717..47404547,2	K562	blood:
20	chr2:38892007..38895113-chr2:38976994..38979857,4	K562	blood:
21	chr2:38975156..38979928-chr2:39002986..39007194,11	MCF-7	breast:
22	chr2:38824770..38827325-chr2:38977013..38980268,3	MCF-7	breast:
23	chr2:38976319..38979796-chr2:38988969..38996616,16	MCF-7	breast:
24	chr2:38977048..38979806-chr2:39045778..39047764,3	MCF-7	breast:
25	chr2:38977749..38979717-chr2:39155350..39158126,2	K562	blood:
26	chr2:38973912..38980240-chr2:38989822..38999883,17	MCF-7	breast:

No data

Variant related genes	Relation type
SRSF7	TF binding region
SRSF7	CpG island
ENSG00000271443	Chromatin interaction
ENSG00000115944	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000227238	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000235586	Chromatin interaction
ENSG00000125812	Chromatin interaction
ENSG00000115816	Chromatin interaction
ENSG00000214694	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000003509	Chromatin interaction
ENSG00000232114	Chromatin interaction
ENSG00000188010	Chromatin interaction
ENSG00000163214	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10173118	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10197412	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10865143	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1138975	0.86[AFR][1000 genomes]
rs11694383	0.81[EUR][1000 genomes]
rs12474770	0.88[ASN][1000 genomes]
rs12477252	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12618118	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12621103	0.90[ASN][1000 genomes]
rs12991609	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13014136	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13024811	0.90[ASN][1000 genomes]
rs13411868	0.86[AMR][1000 genomes]
rs13417196	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2037875	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099971	0.82[ASN][1000 genomes]
rs3112183	0.92[ASN][1000 genomes]
rs3112184	0.82[ASN][1000 genomes]
rs3112186	0.82[ASN][1000 genomes]
rs3112188	0.82[ASN][1000 genomes]
rs3112189	0.82[ASN][1000 genomes]
rs3112191	0.82[ASN][1000 genomes]
rs3112192	0.82[ASN][1000 genomes]
rs3112198	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3112200	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3134628	0.92[ASN][1000 genomes]
rs3134629	0.92[ASN][1000 genomes]
rs3134630	0.92[ASN][1000 genomes]
rs3134637	0.81[ASN][1000 genomes]
rs35387882	0.83[ASN][1000 genomes]
rs4602206	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4630748	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4670892	0.88[ASN][1000 genomes]
rs56393601	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62144837	0.80[AMR][1000 genomes]
rs6715866	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6746818	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6753251	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12472454	SFRS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38978800-38979800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr2:38979000-38981400	Weak transcription	Ovary	ovary
3	chr2:38979200-38979800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:38979200-38979800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr2:38979200-38979800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:38979200-38979800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:38979200-38979800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr2:38979200-38979800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:38979200-38979800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:38979200-38979800	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr2:38979200-38979800	Enhancers	Fetal Lung	lung
12	chr2:38979200-38979800	Flanking Active TSS	HepG2	liver
13	chr2:38979200-38980800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:38979200-38981400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:38979200-38981400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:38979200-38981400	Weak transcription	Right Atrium	heart
17	chr2:38979200-38983800	Weak transcription	HSMM	muscle
18	chr2:38979200-39005000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:38979400-38979800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:38979400-38979800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:38979400-38979800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:38979400-38979800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:38979400-38979800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr2:38979400-38979800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr2:38979400-38979800	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr2:38979400-38980800	Weak transcription	GM12878-XiMat	blood
27	chr2:38979400-38981000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:38979400-38981000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:38979400-38981000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr2:38979400-38981000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:38979400-38981000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:38979400-38981000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:38979400-38981000	Weak transcription	Liver	Liver
34	chr2:38979400-38981000	Weak transcription	Stomach Mucosa	stomach
35	chr2:38979400-38981000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr2:38979400-38981200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:38979400-38981200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr2:38979400-38981200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr2:38979400-38981200	Weak transcription	Primary B cells from cord blood	blood
40	chr2:38979400-38981200	Weak transcription	Adipose Nuclei	Adipose
41	chr2:38979400-38981200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:38979400-38981400	Weak transcription	NHDF-Ad	bronchial
43	chr2:38979400-38981400	Weak transcription	Osteobl	bone
44	chr2:38979400-38981600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:38979600-38979800	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr2:38979600-38979800	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr2:38979600-38979800	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr2:38979600-38979800	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr2:38979600-38979800	Enhancers	A549	lung
50	chr2:38979600-38979800	Enhancers	Dnd41	blood

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