Variant report

Variant	rs12738378
Chromosome Location	chr1:158984322-158984323
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr1:158984303-158985747	MCF10A-Er-Src	breast:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
2	POLR2A	chr1:158982898-158984553	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:158982037-158984384	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:158983699-158984460	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:158982888-158984463	GM12878	blood:	n/a	n/a
6	WRNIP1	chr1:158983831-158984351	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:158983414-158985843	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr1:158983215-158984375	U87	brain:	n/a	n/a
9	POLR2A	chr1:158981852-158987235	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr1:158978464-158986840	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:158983811-158984386	GM12891	blood:	n/a	n/a
12	MYC	chr1:158984174-158985679	MCF10A-Er-Src	breast:	n/a	chr1:158985381-158985391 chr1:158985408-158985418
13	POLR2A	chr1:158983798-158984362	GM12891	blood:	n/a	n/a
14	POLR2A	chr1:158983290-158984427	GM12892	blood:	n/a	n/a
15	POLR2A	chr1:158981523-158987265	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:158983733-158984535	U87	brain:	n/a	n/a
17	POLR2A	chr1:158978384-158985943	GM19193	blood:	n/a	n/a
18	POLR2A	chr1:158983209-158984552	U87	brain:	n/a	n/a
19	ELK1	chr1:158984316-158984419	GM12878	blood:	n/a	n/a
20	EP300	chr1:158984218-158984412	GM12878	blood:	n/a	n/a
21	MXI1	chr1:158983925-158984688	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:158981580-158990399	GM12891	blood:	n/a	n/a
23	POLR2A	chr1:158983734-158984416	GM12892	blood:	n/a	n/a
24	POLR2A	chr1:158981297-158987303	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:158978350-158987224	GM18505	blood:	n/a	n/a
26	POLR2A	chr1:158978475-158987184	GM19099	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:158984321-158984371	BJ	skin:	n/a
2	chr1:158984321-158984371	NHDF-neo	bronchial:	n/a
3	chr1:158984321-158984371	Caco-2	colon:	n/a
4	chr1:158984321-158984371	ovcar-3	ovarian:	n/a
5	chr1:158984321-158984371	HL-60	blood:	n/a
6	chr1:158984321-158984371	PFSK-1	brain:	n/a
7	chr1:158984321-158984371	Jurkat	blood:	n/a
8	chr1:158984321-158984371	PrEC	prostate:	n/a
9	chr1:158984321-158984371	ProgFib	skin:	n/a
10	chr1:158984321-158984371	A549	lung:	n/a
11	chr1:158984321-158984371	T-47D	breast:	n/a
12	chr1:158984321-158984371	GM12878	blood:	n/a
13	chr1:158984321-158984371	NB4	blood:	n/a
14	chr1:158984321-158984371	Hepatocyte	liver:	n/a
15	chr1:158984321-158984371	AG10803	skin:	n/a
16	chr1:158984321-158984371	HRCEpiC	kidney:	n/a
17	chr1:158984321-158984371	GM12891	blood:	n/a
18	chr1:158984321-158984371	GM19239	blood:	n/a
19	chr1:158984321-158984371	HCF	heart:	n/a
20	chr1:158984321-158984371	HEEpiC	esophagus:	n/a
21	chr1:158984321-158984371	SK-N-SH	brain:	n/a
22	chr1:158984321-158984371	HPAEpiC	pulmonary alveolar:	n/a
23	chr1:158984321-158984371	HCT-116	colon:	n/a
24	chr1:158984321-158984371	MCF-7	breast:	n/a
25	chr1:158984321-158984371	NH-A	brain:	n/a
26	chr1:158984321-158984371	AG04450	lung:	fetal
27	chr1:158984321-158984371	AoSMC	blood vessel:	n/a
28	chr1:158984321-158984371	GM12892	blood:	n/a
29	chr1:158984321-158984371	CMK	blood:	n/a
30	chr1:158984321-158984371	HEK293	kidney:	embryo
31	chr1:158984321-158984371	AG09319	gingival:	n/a
32	chr1:158984321-158984371	H1-hESC	embryonic stem cell:	embryo
33	chr1:158984321-158984371	PANC-1	pancreas:	n/a
34	chr1:158984321-158984371	NT2-D1	testis:	n/a
35	chr1:158984321-158984371	AG09309	skin:	n/a
36	chr1:158984321-158984371	HNPCEpiC	eye:	n/a
37	chr1:158984321-158984371	HRPEpiC	eye:	n/a
38	chr1:158984321-158984371	IMR90	lung:	fetal
39	chr1:158984321-158984371	HepG2	liver:	n/a
40	chr1:158984321-158984371	HCM	heart:	n/a
41	chr1:158984321-158984371	HUVEC	blood vessel:	n/a
42	chr1:158984321-158984371	SK-N-MC	brain:	n/a
43	chr1:158984321-158984371	SAEC	small airway:	n/a
44	chr1:158984321-158984371	SKMC	muscle:	n/a
45	chr1:158984321-158984371	HMEC	breast:	n/a
46	chr1:158984321-158984371	HAEpiC	amniotic membrane:	n/a
47	chr1:158984321-158984371	MCF10A-Er-Src	breast:	n/a
48	chr1:158984321-158984371	GM06990	blood:	n/a
49	chr1:158984321-158984371	HIPEpiC	eye:	n/a
50	chr1:158984321-158984371	SK-N-SH_RA	brain:	n/a

No data

Variant related genes	Relation type
IFI16	TF binding region
IFI16	CpG island

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11539423	0.88[AMR][1000 genomes]
rs12727764	0.91[MEX][hapmap]
rs12728586	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12734915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12739704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12755219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1361564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1361565	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16841500	0.88[AMR][1000 genomes]
rs1956	0.88[AMR][1000 genomes]
rs4262539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66519738	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72704976	0.88[AMR][1000 genomes]
rs7526724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs856047	0.85[AMR][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	esv3376764	chr1:158761947-158998617	Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3369957	chr1:158915589-159003393	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv3176	chr1:158955373-158986568	Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv872486	chr1:158979191-159090256	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158976000-159000800	Weak transcription	Gastric	stomach
2	chr1:158977200-158990400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:158978800-158985800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr1:158979400-158984400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:158979400-158984400	Active TSS	Brain Anterior Caudate	brain
6	chr1:158979400-158984400	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr1:158979800-158984600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:158980200-159025400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:158981200-158985400	Weak transcription	Fetal Intestine Small	intestine
10	chr1:158981200-158985400	Weak transcription	Pancreas	Pancrea
11	chr1:158981200-158986400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:158981600-158986000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr1:158982000-158988000	Weak transcription	Fetal Brain Male	brain
14	chr1:158982600-158984400	Active TSS	Brain Substantia Nigra	brain
15	chr1:158982600-158984800	Strong transcription	HSMM	muscle
16	chr1:158982600-158985400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:158982600-158985400	Weak transcription	Brain Angular Gyrus	brain
18	chr1:158982600-158985400	Weak transcription	Fetal Stomach	stomach
19	chr1:158982600-158986200	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:158982600-159027400	Weak transcription	Fetal Kidney	kidney
21	chr1:158982800-158984400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:158982800-158984400	Weak transcription	Fetal Intestine Large	intestine
23	chr1:158982800-158984600	Weak transcription	NHLF	lung
24	chr1:158982800-158984800	Weak transcription	HMEC	breast
25	chr1:158982800-158985000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:158982800-158985200	Weak transcription	Stomach Mucosa	stomach
27	chr1:158982800-158985400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:158982800-158985400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:158982800-158985400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:158982800-158985400	Weak transcription	NH-A	brain
31	chr1:158982800-158987800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:158982800-158989600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:158982800-159000200	Weak transcription	Aorta	Aorta
34	chr1:158983000-158984400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:158983000-158984400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
36	chr1:158983000-158984400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:158983000-158984600	Enhancers	Spleen	Spleen
38	chr1:158983000-158986000	Genic enhancers	Osteobl	bone
39	chr1:158983000-158987200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:158983200-158985400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:158983200-158985400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:158983200-158985400	Weak transcription	Lung	lung
43	chr1:158983200-158986000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:158983400-158984400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
45	chr1:158983400-158984600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:158983400-158984600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr1:158983400-158985200	Genic enhancers	Primary hematopoietic stem cells	blood
48	chr1:158983400-158985400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr1:158983400-158985600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:158983400-158985800	Enhancers	Small Intestine	intestine

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