Variant report

Variant	rs678850
Chromosome Location	chr1:10492168-10492169
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:10492131-10492360	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10473791..10476777-chr1:10490511..10492354,2	K562	blood:
2	chr1:10457794..10460664-chr1:10487844..10492697,5	K562	blood:
3	chr1:10490607..10494447-chr1:10532445..10535163,5	K562	blood:
4	chr1:10488008..10492443-chr1:10531123..10534892,8	K562	blood:
5	chr1:10490085..10492364-chr1:10508772..10511442,3	K562	blood:
6	chr1:10489993..10493018-chr1:10531254..10535234,5	MCF-7	breast:
7	chr1:10490864..10493248-chr1:10508230..10510272,2	K562	blood:
8	chr1:10489448..10493967-chr1:10494423..10498103,7	K562	blood:
9	chr1:10002273..10004549-chr1:10490535..10492203,2	MCF-7	breast:
10	chr1:10457881..10459696-chr1:10491385..10493588,2	MCF-7	breast:

No data

Variant related genes	Relation type
APITD1-CORT	TF binding region
ENSG00000271989	TF binding region
ENSG00000142657	Chromatin interaction
ENSG00000173614	Chromatin interaction
ENSG00000251503	Chromatin interaction
ENSG00000241563	Chromatin interaction
ENSG00000160049	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000142655	Chromatin interaction
ENSG00000228150	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10746494	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11121579	0.80[ASN][1000 genomes]
rs1203122	0.87[EUR][1000 genomes]
rs1307485	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1307487	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1750349	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1760664	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2483684	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2781233	0.86[EUR][1000 genomes]
rs36013615	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs475549	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs481571	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs491880	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs505141	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs517241	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs519472	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520964	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs522029	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs522280	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs524150	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs528713	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs579398	0.92[ASN][1000 genomes]
rs583515	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs585703	0.95[ASN][1000 genomes]
rs586096	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs586223	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597441	0.85[EUR][1000 genomes]
rs628462	0.82[ASN][1000 genomes]
rs632690	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs634358	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs643400	0.89[EUR][1000 genomes]
rs649101	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs649639	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs655271	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs663864	0.80[ASN][1000 genomes]
rs666583	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs667366	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs672606	0.86[EUR][1000 genomes]
rs681448	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs681495	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10491400-10492200	Flanking Active TSS	Hela-S3	cervix
2	chr1:10491400-10493000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:10491400-10493600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:10491400-10504600	Weak transcription	Lung	lung
5	chr1:10491400-10519000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:10491400-10521000	Weak transcription	Ovary	ovary
7	chr1:10491400-10521200	Weak transcription	Aorta	Aorta
8	chr1:10491600-10492200	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr1:10491600-10492200	Enhancers	Stomach Mucosa	stomach
10	chr1:10491600-10492200	Enhancers	Thymus	Thymus
11	chr1:10491600-10492600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:10491600-10492600	Enhancers	Brain Angular Gyrus	brain
13	chr1:10491600-10492600	Enhancers	Fetal Heart	heart
14	chr1:10491600-10492800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:10491600-10492800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:10491600-10492800	Enhancers	Fetal Brain Male	brain
17	chr1:10491600-10492800	Weak transcription	Fetal Lung	lung
18	chr1:10491600-10493000	Enhancers	GM12878-XiMat	blood
19	chr1:10491600-10493200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:10491600-10494000	Weak transcription	Fetal Kidney	kidney
21	chr1:10491600-10496800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:10491600-10500000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr1:10491600-10500400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:10491600-10504600	Weak transcription	HSMMtube	muscle
25	chr1:10491600-10508000	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:10491600-10510200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:10491600-10510200	Weak transcription	Gastric	stomach
28	chr1:10491600-10510400	Weak transcription	Right Atrium	heart
29	chr1:10491600-10511000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:10491600-10511000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:10491600-10511200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:10491600-10516200	Weak transcription	HMEC	breast
33	chr1:10491600-10517800	Weak transcription	Primary T cells from cord blood	blood
34	chr1:10491600-10518000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:10491600-10518000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:10491600-10519200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:10491600-10521200	Weak transcription	Brain Substantia Nigra	brain
38	chr1:10491600-10521200	Weak transcription	Left Ventricle	heart
39	chr1:10491600-10521200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:10491600-10521200	Weak transcription	Spleen	Spleen
41	chr1:10491600-10521400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:10491800-10492200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:10491800-10492200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:10491800-10492200	Enhancers	Stomach Smooth Muscle	stomach
45	chr1:10491800-10492400	Enhancers	Brain Germinal Matrix	brain
46	chr1:10491800-10492600	Enhancers	Fetal Intestine Small	intestine
47	chr1:10491800-10492800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:10491800-10492800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:10491800-10492800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:10491800-10492800	Weak transcription	K562	blood

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