Variant report

Variant	rs12000
Chromosome Location	chr6:28227436-28227437
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr6:28226842-28227442	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:28227433-28227440	MCF-7	breast:	n/a	n/a
3	ELF1	chr6:28226888-28227607	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28227392-28227442	NHBE	bronchial:	n/a
2	chr6:28227392-28227442	IMR90	lung:	fetal
3	chr6:28227392-28227442	AG04449	skin:	fetal
4	chr6:28227392-28227442	SK-N-MC	brain:	n/a
5	chr6:28227392-28227442	Hepatocyte	liver:	n/a
6	chr6:28227392-28227442	A549	lung:	n/a
7	chr6:28227392-28227442	AG09319	gingival:	n/a
8	chr6:28227392-28227442	NT2-D1	testis:	n/a
9	chr6:28227392-28227442	K562	blood:	n/a
10	chr6:28227392-28227442	H1-hESC	embryonic stem cell:	embryo
11	chr6:28227392-28227442	ProgFib	skin:	n/a
12	chr6:28227392-28227442	NH-A	brain:	n/a
13	chr6:28227392-28227442	HL-60	blood:	n/a
14	chr6:28227392-28227442	HRPEpiC	eye:	n/a
15	chr6:28227392-28227442	HCT-116	colon:	n/a
16	chr6:28227392-28227442	HIPEpiC	eye:	n/a
17	chr6:28227392-28227442	ECC-1	luminal epithelium:	n/a
18	chr6:28227392-28227442	HCM	heart:	n/a
19	chr6:28227392-28227442	AG09309	skin:	n/a
20	chr6:28227392-28227442	AoSMC	blood vessel:	n/a
21	chr6:28227392-28227442	NHDF-neo	bronchial:	n/a
22	chr6:28227392-28227442	U87	brain:	n/a
23	chr6:28227392-28227442	GM12892	blood:	n/a
24	chr6:28227392-28227442	AG04450	lung:	fetal
25	chr6:28227392-28227442	T-47D	breast:	n/a
26	chr6:28227392-28227442	PANC-1	pancreas:	n/a
27	chr6:28227392-28227442	Hela-S3	cervix:	n/a
28	chr6:28227392-28227442	HAEpiC	amniotic membrane:	n/a
29	chr6:28227392-28227442	HCF	heart:	n/a
30	chr6:28227392-28227442	NB4	blood:	n/a
31	chr6:28227392-28227442	GM06990	blood:	n/a
32	chr6:28227392-28227442	HNPCEpiC	eye:	n/a
33	chr6:28227392-28227442	GM12878	blood:	n/a
34	chr6:28227392-28227442	LNCaP	prostate:	n/a
35	chr6:28227392-28227442	HRCEpiC	kidney:	n/a
36	chr6:28227392-28227442	CMK	blood:	n/a
37	chr6:28227392-28227442	Caco-2	colon:	n/a
38	chr6:28227392-28227442	SK-N-SH_RA	brain:	n/a
39	chr6:28227392-28227442	PrEC	prostate:	n/a
40	chr6:28227392-28227442	ovcar-3	ovarian:	n/a
41	chr6:28227392-28227442	HRE	kidney:	n/a
42	chr6:28227392-28227442	SK-N-SH	brain:	n/a
43	chr6:28227392-28227442	GM12891	blood:	n/a
44	chr6:28227392-28227442	PFSK-1	brain:	n/a
45	chr6:28227392-28227442	HPAEpiC	pulmonary alveolar:	n/a
46	chr6:28227392-28227442	SAEC	small airway:	n/a
47	chr6:28227392-28227442	GM19239	blood:	n/a
48	chr6:28227392-28227442	RPTEC	kidney:	n/a
49	chr6:28227392-28227442	HCPEpiC	choroid plexus:	n/a
50	chr6:28227392-28227442	HMEC	breast:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr6:28219997..28223882-chr6:28224379..28228192,5	K562	blood:
2	chr6:28226019..28228390-chr6:28303494..28305290,2	K562	blood:
3	chr6:28225119..28227553-chr6:28366156..28368716,2	K562	blood:
4	chr6:28218888..28222826-chr6:28224722..28227606,3	K562	blood:
5	chr6:28217539..28222258-chr6:28227412..28230016,4	MCF-7	breast:

No data

Variant related genes	Relation type
ZKSCAN4	TF binding region
ZKSCAN4	CpG island
ENSG00000235109	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000187626	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11965538	0.84[YRI][hapmap]
rs12180820	0.86[CHB][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap]
rs13200462	0.80[YRI][hapmap]
rs1416920	0.86[CHB][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap]
rs1419183	0.84[YRI][hapmap]
rs1635	0.80[CHB][hapmap]
rs1679709	0.80[LWK][hapmap];0.84[YRI][hapmap]
rs16893889	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1778508	0.84[YRI][hapmap]
rs2108926	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2179174	1.00[CEU][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2799077	0.84[YRI][hapmap]
rs2799079	0.91[YRI][hapmap]
rs6901575	0.84[YRI][hapmap]
rs6936644	0.84[ASN][1000 genomes]
rs6942030	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs758398	0.80[CHB][hapmap]
rs7750106	0.81[CHB][hapmap]
rs9468334	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9468344	0.86[CHB][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12000	ZNF187	cis	cerebellum	SCAN
rs12000	ZKSCAN3	cis	parietal	SCAN
rs12000	ZNF323	cis	cerebellum	SCAN
rs12000	HIST1H4C	cis	parietal	SCAN
rs12000	AL022393.7	cis	Thyroid	GTEx
rs12000	ZNF165	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28225800-28227800	Active TSS	Colon Smooth Muscle	Colon
2	chr6:28226200-28228200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
3	chr6:28226400-28227600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:28226400-28227600	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr6:28226400-28227600	ZNF genes & repeats	Liver	Liver
6	chr6:28226400-28227600	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr6:28226400-28227600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr6:28226400-28227600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr6:28226400-28227800	Active TSS	Brain Anterior Caudate	brain
10	chr6:28226600-28227600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:28226600-28227600	ZNF genes & repeats	Primary B cells from cord blood	blood
12	chr6:28226600-28227600	Active TSS	Brain Angular Gyrus	brain
13	chr6:28226600-28227600	Active TSS	Brain Cingulate Gyrus	brain
14	chr6:28226600-28227600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:28226600-28227600	Active TSS	Duodenum Mucosa	Duodenum
16	chr6:28226600-28227600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
17	chr6:28226600-28227600	Active TSS	Left Ventricle	heart
18	chr6:28226600-28227600	ZNF genes & repeats	HMEC	breast
19	chr6:28226600-28227600	ZNF genes & repeats	NHEK	skin
20	chr6:28226600-28227800	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr6:28226600-28228400	Active TSS	Psoas Muscle	Psoas
22	chr6:28226800-28227600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr6:28226800-28227600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:28226800-28227600	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr6:28226800-28227600	Active TSS	Colonic Mucosa	Colon
26	chr6:28226800-28227600	Bivalent/Poised TSS	Fetal Brain Female	brain
27	chr6:28226800-28227600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
28	chr6:28226800-28227600	ZNF genes & repeats	Placenta	Placenta
29	chr6:28226800-28227600	ZNF genes & repeats	Lung	lung
30	chr6:28226800-28227600	Flanking Active TSS	Pancreas	Pancrea
31	chr6:28226800-28227600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
32	chr6:28226800-28227800	Bivalent/Poised TSS	Fetal Kidney	kidney
33	chr6:28227000-28227600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:28227000-28227600	ZNF genes & repeats	Gastric	stomach
35	chr6:28227000-28227600	ZNF genes & repeats	Spleen	Spleen
36	chr6:28227000-28227600	ZNF genes & repeats	NHDF-Ad	bronchial
37	chr6:28227000-28228400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:28227000-28232000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr6:28227000-28233800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr6:28227200-28227600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:28227200-28227600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:28227200-28227600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:28227200-28227600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
44	chr6:28227200-28227600	Flanking Bivalent TSS/Enh	Fetal Heart	heart
45	chr6:28227200-28227600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
46	chr6:28227200-28227600	Bivalent/Poised TSS	Fetal Stomach	stomach
47	chr6:28227200-28227600	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr6:28227200-28227600	Flanking Active TSS	Right Ventricle	heart
49	chr6:28227200-28227600	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr6:28227200-28227600	Active TSS	Osteobl	bone

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