Variant report

Variant	rs11811190
Chromosome Location	chr1:174966816-174966817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:174965583-174970714	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:174966244-174967528	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:174963970-174972111	K562	blood:	n/a	n/a
4	NFATC1	chr1:174964816-174966938	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:174966326-174969439	GM12891	blood:	n/a	n/a
6	POLR2A	chr1:174966429-174967461	GM12892	blood:	n/a	n/a
7	MTA3	chr1:174965552-174970296	GM12878	blood:	n/a	n/a
8	NFATC1	chr1:174966038-174967357	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:174965683-174969692	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:174965744-174969756	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr1:174966812-174969997	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:174940560..174943499-chr1:174966339..174968094,3	K562	blood:
2	chr1:174922181..174924698-chr1:174966768..174969386,2	K562	blood:
3	chr1:174932418..174935374-chr1:174964535..174970014,5	K562	blood:
4	chr1:174846552..174849289-chr1:174966305..174968766,3	K562	blood:
5	chr1:174823652..174825936-chr1:174966257..174968249,2	MCF-7	breast:
6	chr1:174966465..174968007-chr1:174970965..174973643,2	MCF-7	breast:
7	chr1:174849491..174851147-chr1:174966339..174967992,2	K562	blood:
8	chr1:174966455..174979047-chr1:174985921..174994239,29	MCF-7	breast:
9	chr1:174838028..174843892-chr1:174965943..174969167,5	K562	blood:
10	chr1:174935713..174937264-chr1:174965663..174967538,2	K562	blood:
11	chr1:174923198..174925384-chr1:174966768..174969238,3	K562	blood:
12	chr1:174927580..174945830-chr1:174955726..174971213,32	K562	blood:
13	chr1:174840446..174846237-chr1:174965266..174970099,5	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPS14-1	chr1:174966629-174966870	XLOC_001097
2	lnc-MRPS14-1	chr1:174966616-174966870	NONHSAT007744
3	lnc-MRPS14-1	chr1:174964447-174968075	NONHSAT007742

No data

Variant related genes	Relation type
CACYBP	TF binding region
ENSG00000120333	Chromatin interaction
ENSG00000229531	Chromatin interaction
ENSG00000152061	Chromatin interaction
ENSG00000206659	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10489330	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489332	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12140378	0.84[ASN][1000 genomes]
rs12737503	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16847730	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2861102	0.84[ASN][1000 genomes]
rs3753562	0.80[AFR][1000 genomes]
rs41266060	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41266064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41498747	0.80[AFR][1000 genomes]
rs57053120	0.80[AFR][1000 genomes]
rs58618779	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58762254	0.84[AFR][1000 genomes]
rs60893569	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1001000	chr1:174944208-174978853	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11811190	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174924200-174967800	Weak transcription	Brain Germinal Matrix	brain
2	chr1:174935000-174967000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:174940000-174967600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:174941000-174968000	Weak transcription	Gastric	stomach
5	chr1:174944400-174967800	Weak transcription	Aorta	Aorta
6	chr1:174944800-174967800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:174944800-174968000	Weak transcription	Spleen	Spleen
8	chr1:174946000-174968000	Weak transcription	Lung	lung
9	chr1:174949000-174967800	Weak transcription	Fetal Stomach	stomach
10	chr1:174952200-174967800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:174952400-174968000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:174954800-174968000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:174956000-174967800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:174956200-174967400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:174959600-174967400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:174960000-174967200	Weak transcription	Fetal Thymus	thymus
17	chr1:174960000-174967200	Weak transcription	Left Ventricle	heart
18	chr1:174960000-174967800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:174960000-174968000	Weak transcription	Esophagus	oesophagus
20	chr1:174960200-174967000	Weak transcription	Primary T cells from cord blood	blood
21	chr1:174960200-174967000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr1:174960200-174967000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:174960200-174967200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr1:174960200-174967200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr1:174960200-174967200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:174960200-174967200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:174960200-174967200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:174960200-174967400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:174960200-174967400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:174960200-174967400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:174960200-174967400	Weak transcription	A549	lung
32	chr1:174960200-174967600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:174960200-174967600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:174960200-174967600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:174960200-174967600	Weak transcription	Thymus	Thymus
36	chr1:174960200-174967800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:174960200-174967800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:174960200-174967800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:174960200-174967800	Weak transcription	Fetal Muscle Leg	muscle
40	chr1:174960200-174967800	Weak transcription	HSMMtube	muscle
41	chr1:174960400-174967800	Weak transcription	Adipose Nuclei	Adipose
42	chr1:174960600-174967200	Weak transcription	Primary B cells from cord blood	blood
43	chr1:174960600-174967400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:174960600-174967600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:174960800-174967400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:174961400-174967800	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:174961600-174967800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr1:174962000-174967800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:174962800-174967200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr1:174963200-174967600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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