Variant report

Variant	rs10889868
Chromosome Location	chr1:70816563-70816564
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:70815891-70816932	K562	blood:	n/a	n/a
2	POLR2A	chr1:70816489-70816818	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:70815918-70816987	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:70686767..70689766-chr1:70815216..70817430,2	K562	blood:
2	chr1:70814888..70817395-chr1:70819218..70821847,2	MCF-7	breast:
3	chr1:70799533..70801212-chr1:70816344..70819008,2	K562	blood:
4	chr1:70814842..70821925-chr1:70874223..70879265,8	K562	blood:
5	chr1:70814864..70817394-chr1:70817734..70820008,3	MCF-7	breast:

Variant related genes	Relation type
HHLA3	TF binding region
ENSG00000118454	Chromatin interaction
ENSG00000116761	Chromatin interaction
ENSG00000197568	Chromatin interaction
ENSG00000116754	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11209600	0.81[CHD][hapmap]
rs11209605	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11209606	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12036256	0.86[CHD][hapmap]
rs12037272	0.86[CHD][hapmap]
rs1969953	0.81[CHB][hapmap]
rs2149030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4560989	0.81[CHD][hapmap]
rs4650041	0.86[CHD][hapmap]
rs61782670	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6686181	0.81[CHD][hapmap]
rs7512277	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7539544	0.81[CHD][hapmap]
rs768433	0.81[CHD][hapmap]
rs998523	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv1012563	chr1:70753332-70832118	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1792702	chr1:70755511-70818576	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1801665	chr1:70755511-70832053	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv871430	chr1:70765659-70819912	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10889868	CTH	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70688000-70819200	Weak transcription	Esophagus	oesophagus
2	chr1:70760600-70818200	Weak transcription	Aorta	Aorta
3	chr1:70760600-70818600	Weak transcription	Thymus	Thymus
4	chr1:70762000-70817600	Weak transcription	NHLF	lung
5	chr1:70762200-70818200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:70765600-70818200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:70767800-70819000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:70768200-70817000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:70770400-70817200	Weak transcription	Pancreas	Pancrea
10	chr1:70773600-70818200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:70773800-70818200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:70774200-70818000	Weak transcription	Fetal Kidney	kidney
13	chr1:70784200-70817400	Weak transcription	Small Intestine	intestine
14	chr1:70787400-70817600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:70788600-70818200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:70789200-70818200	Weak transcription	Right Atrium	heart
17	chr1:70790600-70818000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:70790600-70818400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:70793600-70818000	Weak transcription	NH-A	brain
20	chr1:70794400-70818000	Weak transcription	HMEC	breast
21	chr1:70799400-70818000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:70799600-70817600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:70799600-70818000	Weak transcription	K562	blood
24	chr1:70799600-70818600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:70800400-70817000	Weak transcription	Adipose Nuclei	Adipose
26	chr1:70800400-70817600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:70800400-70817600	Weak transcription	NHDF-Ad	bronchial
28	chr1:70800400-70818200	Weak transcription	Primary B cells from cord blood	blood
29	chr1:70800400-70818200	Weak transcription	HSMM	muscle
30	chr1:70800400-70818400	Weak transcription	Fetal Intestine Large	intestine
31	chr1:70800400-70819200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:70800400-70819200	Weak transcription	Placenta	Placenta
33	chr1:70800600-70817200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:70801000-70817600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:70801000-70817600	Weak transcription	Left Ventricle	heart
36	chr1:70804200-70816600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr1:70804800-70818000	Weak transcription	Osteobl	bone
38	chr1:70804800-70818200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:70804800-70818200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:70804800-70818200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr1:70805000-70818200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:70805000-70819000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:70809400-70819400	Weak transcription	Spleen	Spleen
44	chr1:70809600-70816600	Weak transcription	Psoas Muscle	Psoas
45	chr1:70809600-70818400	Weak transcription	Fetal Thymus	thymus
46	chr1:70810000-70816600	Weak transcription	Lung	lung
47	chr1:70810400-70818800	Weak transcription	Fetal Muscle Leg	muscle
48	chr1:70811200-70818200	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr1:70811600-70819000	Weak transcription	Stomach Mucosa	stomach
50	chr1:70812200-70818200	Weak transcription	Ovary	ovary

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