Variant report

Variant	rs2043542
Chromosome Location	chr2:11639663-11639664
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11639160..11641163-chr2:11820706..11822536,2	MCF-7	breast:
2	chr12:131506010..131507766-chr2:11639592..11642275,2	MCF-7	breast:
3	chr2:11624474..11626052-chr2:11639612..11642018,2	K562	blood:
4	chr2:11272830..11274670-chr2:11637481..11640163,2	MCF-7	breast:
5	chr2:11483004..11485278-chr2:11638232..11641196,2	MCF-7	breast:
6	chr2:11638999..11641397-chr2:11660488..11662917,2	K562	blood:

Variant related genes	Relation type
ENSG00000228496	Chromatin interaction
ENSG00000150873	Chromatin interaction
ENSG00000145063	Chromatin interaction
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10169987	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174895	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192123	1.00[ASN][1000 genomes]
rs10201673	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205078	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929750	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897533	1.00[ASN][1000 genomes]
rs12165170	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13383410	0.86[ASN][1000 genomes]
rs13388093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13395155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13407457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13418262	0.86[ASN][1000 genomes]
rs13424905	0.86[ASN][1000 genomes]
rs13430148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1595018	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16857565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16857586	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2002730	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2082829	1.00[ASN][1000 genomes]
rs2082830	1.00[ASN][1000 genomes]
rs4668729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669736	1.00[EUR][1000 genomes]
rs4669737	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669739	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669740	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669741	0.87[ASN][1000 genomes]
rs58651473	1.00[EUR][1000 genomes]
rs61362255	0.86[ASN][1000 genomes]
rs6432202	1.00[CHB][hapmap]
rs6432209	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728365	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs6739168	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741736	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756327	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73187472	0.86[ASN][1000 genomes]
rs7566661	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7597108	0.86[ASN][1000 genomes]
rs7597865	1.00[EUR][1000 genomes]
rs875231	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877164	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2043542	RASIP1	trans	lymphoblastoid	seeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11636400-11646400	Weak transcription	Right Atrium	heart
2	chr2:11636600-11639800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr2:11636600-11641200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:11637000-11640800	Enhancers	Liver	Liver
5	chr2:11637400-11640200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:11637800-11640000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:11638200-11640200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr2:11638400-11640000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr2:11638400-11640000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr2:11638600-11639800	Enhancers	Adipose Nuclei	Adipose
11	chr2:11638600-11639800	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr2:11638600-11639800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
13	chr2:11638600-11639800	Enhancers	Fetal Muscle Leg	muscle
14	chr2:11638600-11639800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr2:11638600-11639800	Flanking Active TSS	GM12878-XiMat	blood
16	chr2:11638600-11639800	Enhancers	HSMMtube	muscle
17	chr2:11638600-11640000	Enhancers	Fetal Lung	lung
18	chr2:11638800-11639800	Enhancers	Fetal Stomach	stomach
19	chr2:11638800-11640000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr2:11638800-11640000	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr2:11638800-11640000	Enhancers	Fetal Kidney	kidney
22	chr2:11638800-11641400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr2:11638800-11646200	Weak transcription	Psoas Muscle	Psoas
24	chr2:11639000-11639800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr2:11639000-11639800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr2:11639000-11639800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:11639000-11640000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:11639000-11640600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:11639400-11639800	Flanking Active TSS	Fetal Heart	heart
30	chr2:11639400-11640000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:11639400-11640000	Enhancers	Brain Cingulate Gyrus	brain
32	chr2:11639400-11640800	Weak transcription	A549	lung
33	chr2:11639600-11639800	Enhancers	Brain Anterior Caudate	brain
34	chr2:11639600-11639800	Enhancers	Ovary	ovary
35	chr2:11639600-11640000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr2:11639600-11640000	Flanking Active TSS	HepG2	liver
37	chr2:11639600-11640200	Enhancers	Brain Substantia Nigra	brain
38	chr2:11639600-11640600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:11639600-11640800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:11639600-11641000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:11639600-11641000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr2:11639600-11641000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:11639600-11641000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr2:11639600-11641200	Weak transcription	Colonic Mucosa	Colon
45	chr2:11639600-11643000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:11639600-11643400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr2:11639600-11645400	Weak transcription	Pancreas	Pancrea
48	chr2:11639600-11646000	Weak transcription	Hela-S3	cervix
49	chr2:11639600-11646400	Weak transcription	Right Ventricle	heart
50	chr2:11639600-11647600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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