Variant report

Variant	rs35930163
Chromosome Location	chr1:171768184-171768185
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	chr1:171767253-171768989	Hela-S3	cervix:	n/a	n/a
2	GATA3	chr1:171768040-171768803	MCF-7	breast:	n/a	chr1:171768632-171768639 chr1:171768632-171768639 chr1:171768629-171768639 chr1:171768516-171768529 chr1:171768632-171768639
3	POLR2A	chr1:171768111-171768552	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:171766142-171769839	K562	blood:	n/a	n/a
5	POLR2A	chr1:171768182-171768395	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:171767456-171768660	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:171750108..171754190-chr1:171766349..171769659,4	K562	blood:
2	chr1:171760261..171763188-chr1:171766979..171768595,2	MCF-7	breast:
3	chr1:171764717..171768373-chr1:171769892..171773572,7	K562	blood:
4	chr1:171768042..171770155-chr1:171772867..171774422,2	MCF-7	breast:
5	chr1:171709806..171712029-chr1:171768013..171770054,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213060	TF binding region
ENSG00000117533	Chromatin interaction
ENSG00000010165	Chromatin interaction
ENSG00000213060	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1045456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489252	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12091786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565176	0.98[EUR][1000 genomes]
rs12567851	0.87[EUR][1000 genomes]
rs12730717	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12742601	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12750330	0.88[EUR][1000 genomes]
rs12753043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17596025	0.99[EUR][1000 genomes]
rs17596081	0.99[EUR][1000 genomes]
rs17649609	0.98[EUR][1000 genomes]
rs17650310	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17650340	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17657363	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1801898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143369	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181216	0.99[EUR][1000 genomes]
rs2223602	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2232807	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232813	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232819	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232825	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236894	0.81[EUR][1000 genomes]
rs236897	0.86[EUR][1000 genomes]
rs236898	0.86[EUR][1000 genomes]
rs236899	0.85[EUR][1000 genomes]
rs236900	0.87[EUR][1000 genomes]
rs34320898	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34627492	0.88[EUR][1000 genomes]
rs35249022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35400839	0.99[EUR][1000 genomes]
rs35631282	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35674909	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35882887	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36080557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3891278	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55732843	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56365362	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56377810	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61807979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656852	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674364	0.98[EUR][1000 genomes]
rs6675708	0.98[EUR][1000 genomes]
rs6681322	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6689125	0.94[EUR][1000 genomes]
rs6695933	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7522582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription 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	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35930163	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171751600-171770800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:171752000-171773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:171752200-171768200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr1:171752800-171770200	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr1:171754200-171769600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:171754200-171770200	Strong transcription	Primary T cells from cord blood	blood
7	chr1:171754200-171770200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:171754400-171768200	Strong transcription	Left Ventricle	heart
9	chr1:171754800-171768200	Strong transcription	Fetal Thymus	thymus
10	chr1:171754800-171768600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:171754800-171768800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:171755400-171768200	Strong transcription	Spleen	Spleen
13	chr1:171758600-171768400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:171763400-171768200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:171763800-171770400	Weak transcription	Small Intestine	intestine
16	chr1:171764000-171768200	Strong transcription	HSMM	muscle
17	chr1:171765000-171774600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:171765600-171770800	Weak transcription	Hela-S3	cervix
19	chr1:171766000-171768200	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:171766000-171772800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:171766000-171774800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:171766200-171768200	Weak transcription	Fetal Intestine Small	intestine
23	chr1:171766200-171769000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:171766200-171774400	Weak transcription	Brain Substantia Nigra	brain
25	chr1:171766200-171774600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:171766200-171774600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:171766200-171775400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:171766200-171777200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:171766400-171770200	Weak transcription	NH-A	brain
30	chr1:171766400-171777200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:171766600-171768400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:171766600-171770200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:171766600-171770800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:171766600-171774600	Weak transcription	Ovary	ovary
35	chr1:171766600-171774800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:171766600-171774800	Weak transcription	Placenta	Placenta
37	chr1:171766600-171774800	Weak transcription	HepG2	liver
38	chr1:171766800-171768200	Weak transcription	Fetal Heart	heart
39	chr1:171766800-171770400	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:171766800-171770400	Weak transcription	Fetal Kidney	kidney
41	chr1:171766800-171771800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:171766800-171772800	Weak transcription	Right Ventricle	heart
43	chr1:171766800-171774600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:171766800-171774600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr1:171767000-171769000	Weak transcription	HSMMtube	muscle
46	chr1:171767000-171769200	Weak transcription	Colonic Mucosa	Colon
47	chr1:171767000-171770400	Weak transcription	Brain Angular Gyrus	brain
48	chr1:171767000-171770800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:171767000-171770800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr1:171767000-171771600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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