Variant report

Variant	rs7979131
Chromosome Location	chr12:48280455-48280456
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:48280362-48280652	GM12878	blood:	n/a	n/a
2	CTCF	chr12:48280440-48280590	AoAF	blood vessel:	n/a	n/a
3	CTCF	chr12:48280420-48280570	AG04450	lung:	n/a	n/a
4	CTCF	chr12:48280340-48280490	GM12872	blood:	n/a	n/a
5	CTCF	chr12:48280380-48280530	HA-sp	spinal cord:	n/a	n/a
6	CTCF	chr12:48280380-48280530	BJ	skin:	n/a	n/a
7	CTCF	chr12:48280320-48280470	RPTEC	kidney:	n/a	n/a
8	CTCF	chr12:48280440-48280590	HCPEpiC	choroid plexus:	n/a	n/a
9	CTCF	chr12:48280400-48280550	HPF	lung:	n/a	n/a
10	CTCF	chr12:48280336-48280659	IMR90	lung:	n/a	n/a
11	RCOR1	chr12:48280403-48280484	K562	blood:	n/a	n/a
12	CTCF	chr12:48280400-48280550	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr12:48280327-48280679	K562	blood:	n/a	n/a
14	CTCF	chr12:48280400-48280550	HPAF	blood vessel:	n/a	n/a
15	RAD21	chr12:48280313-48280559	GM12878	blood:	n/a	n/a
16	CTCF	chr12:48280440-48280590	A549	lung:	n/a	n/a
17	CTCF	chr12:48280441-48280559	K562	blood:	n/a	n/a
18	CTCF	chr12:48280420-48280570	HVMF	connective:	n/a	n/a
19	CTCF	chr12:48280400-48280550	HMEC	breast:	n/a	n/a
20	CTCF	chr12:48280380-48280530	HVMF	connective:	n/a	n/a
21	CTCF	chr12:48280420-48280570	HPF	lung:	n/a	n/a
22	CTCF	chr12:48280360-48280510	AG04449	skin:	n/a	n/a
23	CTCF	chr12:48280400-48280550	HRE	kidney:	n/a	n/a
24	CTCF	chr12:48280440-48280590	HBMEC	blood vessel:	n/a	n/a
25	CTCF	chr12:48280420-48280570	AoAF	blood vessel:	n/a	n/a
26	CTCF	chr12:48280420-48280570	AG09319	gingival:	n/a	n/a
27	CTCF	chr12:48280420-48280570	AG09309	skin:	n/a	n/a
28	CTCF	chr12:48280300-48280550	NHLF	lung:	n/a	n/a
29	CTCF	chr12:48280441-48280555	MCF-7	breast:	n/a	n/a
30	CTCF	chr12:48280420-48280570	HCPEpiC	choroid plexus:	n/a	n/a
31	CTCF	chr12:48280380-48280530	HMF	breast:	n/a	n/a
32	CTCF	chr12:48280380-48280530	AG10803	skin:	n/a	n/a
33	CTCF	chr12:48280440-48280590	HPAF	blood vessel:	n/a	n/a
34	CTCF	chr12:48280446-48280543	Hela-S3	cervix:	n/a	n/a
35	CTCF	chr12:48280420-48280570	NHDF-neo	bronchial:	n/a	n/a
36	CTCF	chr12:48280440-48280590	HCM	heart:	n/a	n/a
37	CTCF	chr12:48280420-48280570	HMF	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48263786..48264621-chr12:48279992..48280831,3	MCF-7	breast:

No data

Variant related genes	Relation type
VDR	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1989969	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2853559	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2853564	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7965266	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7965274	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48262000-48296800	Weak transcription	Aorta	Aorta
2	chr12:48265000-48283200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:48277000-48286200	Weak transcription	Right Atrium	heart
4	chr12:48277200-48289600	Weak transcription	Esophagus	oesophagus
5	chr12:48277200-48290600	Weak transcription	Gastric	stomach
6	chr12:48277200-48295000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:48277400-48280800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:48277400-48282200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr12:48277600-48280600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr12:48277600-48281200	Weak transcription	HSMMtube	muscle
11	chr12:48277600-48282200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr12:48277600-48287400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:48277600-48289000	Weak transcription	Hela-S3	cervix
14	chr12:48277800-48283000	Weak transcription	Primary B cells from cord blood	blood
15	chr12:48278400-48282400	Weak transcription	Small Intestine	intestine
16	chr12:48278400-48282400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:48278400-48283000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr12:48278400-48287400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:48278400-48289600	Weak transcription	Stomach Mucosa	stomach
20	chr12:48278600-48287800	Strong transcription	NHEK	skin
21	chr12:48278800-48280800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:48278800-48281200	Enhancers	Duodenum Mucosa	Duodenum
23	chr12:48279000-48280800	Enhancers	Osteobl	bone
24	chr12:48279000-48281400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:48279200-48285800	Weak transcription	Colonic Mucosa	Colon
26	chr12:48279200-48286000	Weak transcription	Lung	lung
27	chr12:48279200-48287400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:48279400-48280800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:48279400-48280800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:48279400-48281400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:48279400-48281600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:48279400-48282400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:48279400-48282800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr12:48279400-48283000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:48279400-48283200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:48279400-48283200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:48279400-48283200	Weak transcription	Placenta	Placenta
38	chr12:48279400-48286600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:48279600-48280800	Enhancers	GM12878-XiMat	blood
40	chr12:48279600-48280800	Enhancers	NHDF-Ad	bronchial
41	chr12:48279600-48283000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr12:48279800-48280600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:48279800-48281400	Weak transcription	Fetal Intestine Large	intestine
44	chr12:48279800-48282200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:48279800-48282400	Weak transcription	Spleen	Spleen
46	chr12:48279800-48282600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr12:48279800-48282800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr12:48279800-48283000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:48279800-48283000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr12:48279800-48283000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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