Variant report

Variant	rs941987
Chromosome Location	chr1:173840799-173840800
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	USF1	chr1:173840618-173840995	K562	blood:	n/a	chr1:173840830-173840843 chr1:173840832-173840841 chr1:173840831-173840840 chr1:173840826-173840847 chr1:173840832-173840841
2	CTCF	chr1:173840660-173840810	GM12874	blood:	n/a	n/a
3	JUN	chr1:173832403-173840952	K562	blood:	n/a	chr1:173837048-173837062 chr1:173840939-173840951 chr1:173837421-173837430 chr1:173837165-173837178 chr1:173837443-173837452 chr1:173833568-173833581 chr1:173837835-173837844 chr1:173840672-173840683 chr1:173837169-173837178
4	TEAD4	chr1:173839397-173840806	K562	blood:	n/a	n/a
5	USF1	chr1:173840563-173841004	K562	blood:	n/a	chr1:173840830-173840843 chr1:173840832-173840841 chr1:173840831-173840840 chr1:173840826-173840847 chr1:173840832-173840841
6	STAT3	chr1:173840777-173840910	GM12878	blood:	n/a	n/a
7	BHLHE40	chr1:173840495-173840924	K562	blood:	n/a	chr1:173840830-173840843 chr1:173840832-173840841 chr1:173840831-173840840 chr1:173840826-173840847 chr1:173840832-173840841
8	ZNF384	chr1:173840219-173840901	K562	blood:	n/a	n/a
9	CTCF	chr1:173840542-173840840	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:173837529..173841751-chr1:173936779..173939459,3	K562	blood:
2	chr1:173840096..173840820-chr1:174043690..174044494,2	MCF-7	breast:
3	chr1:173789473..173804179-chr1:173828884..173842109,95	K562	blood:

Variant related genes	Relation type
GAS5	TF binding region
ENSG00000200755	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000117593	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs16846433	0.87[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap]
rs16846478	0.83[EUR][1000 genomes]
rs16846526	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs16846546	0.87[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs16846561	0.87[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs16846593	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2065170	1.00[ASW][hapmap];0.87[CEU][hapmap];0.88[GIH][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2068871	0.87[CEU][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap]
rs2146372	0.96[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2227589	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2227592	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2235095	0.83[EUR][1000 genomes]
rs2759328	1.00[ASW][hapmap];0.87[CEU][hapmap];0.88[GIH][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3791022	0.87[CEU][hapmap]
rs57022387	0.83[EUR][1000 genomes]
rs58994962	0.83[EUR][1000 genomes]
rs61262741	0.83[EUR][1000 genomes]
rs6685043	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs6790	0.83[EUR][1000 genomes]
rs941988	1.00[ASW][hapmap];0.87[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9970048	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs941987	dJ383J4.3	cis	multi-tissue	Pritchard
rs941987		cis	Lymphoblastoid	GTEx
rs941987	CENPL	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173838000-173840800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:173838200-173846600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:173838200-173854200	Weak transcription	Gastric	stomach
4	chr1:173838200-173866000	Weak transcription	Small Intestine	intestine
5	chr1:173838400-173841000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr1:173838400-173844600	Weak transcription	Ovary	ovary
7	chr1:173838400-173844800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:173838400-173854200	Weak transcription	Esophagus	oesophagus
9	chr1:173838400-173854800	Weak transcription	Aorta	Aorta
10	chr1:173838400-173854800	Weak transcription	Right Ventricle	heart
11	chr1:173838400-173860200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:173838600-173841000	Enhancers	Stomach Mucosa	stomach
13	chr1:173838600-173854800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:173838800-173841000	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr1:173838800-173843600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:173838800-173844400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:173838800-173855800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:173839000-173848400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:173839000-173850000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:173839000-173854800	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:173839000-173862800	Weak transcription	HMEC	breast
22	chr1:173839200-173850000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:173839200-173855000	Weak transcription	A549	lung
24	chr1:173839400-173840800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:173839400-173840800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
26	chr1:173839400-173840800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:173839400-173840800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:173839400-173840800	Genic enhancers	Liver	Liver
29	chr1:173839400-173840800	Genic enhancers	Brain Angular Gyrus	brain
30	chr1:173839400-173840800	Genic enhancers	Brain Cingulate Gyrus	brain
31	chr1:173839400-173840800	Genic enhancers	Brain Inferior Temporal Lobe	brain
32	chr1:173839400-173840800	Enhancers	Pancreas	Pancrea
33	chr1:173839400-173840800	Enhancers	Right Atrium	heart
34	chr1:173839400-173840800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
35	chr1:173839400-173840800	Enhancers	Spleen	Spleen
36	chr1:173839400-173840800	Strong transcription	HSMMtube	muscle
37	chr1:173839400-173840800	Strong transcription	NHLF	lung
38	chr1:173839400-173841000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:173839400-173841000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:173839400-173841000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:173839400-173841000	Genic enhancers	Dnd41	blood
42	chr1:173839400-173841000	Genic enhancers	HepG2	liver
43	chr1:173839400-173841400	Genic enhancers	Primary B cells from peripheral blood	blood
44	chr1:173839400-173841600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:173839400-173844000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:173839400-173847800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr1:173839400-173847800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:173839400-173849200	Strong transcription	Fetal Stomach	stomach
49	chr1:173839400-173850000	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:173839600-173840800	Strong transcription	Primary T cells from cord blood	blood

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