Variant report

Variant	rs6542074
Chromosome Location	chr2:113429752-113429753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113407380..113410271-chr2:113429296..113431404,3	K562	blood:
2	chr2:113396469..113398021-chr2:113429600..113431477,2	K562	blood:
3	chr2:113429636..113432230-chr2:113444046..113446844,2	K562	blood:
4	chr2:113422855..113425546-chr2:113428283..113429870,2	K562	blood:

Variant related genes	Relation type
ENSG00000144136	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10167360	0.87[ASN][1000 genomes]
rs10184339	0.94[ASN][1000 genomes]
rs1053652	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10758	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10779885	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11123146	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11680446	0.88[CHB][hapmap]
rs11889567	0.87[ASN][1000 genomes]
rs12467747	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12475403	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12479380	0.80[CEU][hapmap]
rs12612089	0.85[ASN][1000 genomes]
rs12612238	0.87[ASN][1000 genomes]
rs12618806	0.87[ASN][1000 genomes]
rs13023016	0.83[CHB][hapmap]
rs17515708	0.89[ASN][1000 genomes]
rs17515715	0.89[ASN][1000 genomes]
rs2048873	0.89[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs34282612	1.00[ASN][1000 genomes]
rs3827758	0.92[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4261730	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4368335	0.82[CEU][hapmap]
rs4848288	0.81[JPT][hapmap]
rs4849084	0.83[CHB][hapmap]
rs4849086	0.94[CHB][hapmap]
rs4849091	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4849097	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57033895	0.84[EUR][1000 genomes]
rs58662040	0.94[ASN][1000 genomes]
rs58797970	0.84[EUR][1000 genomes]
rs60372418	0.83[ASN][1000 genomes]
rs6705487	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[ASN][1000 genomes]
rs6725228	0.86[ASN][1000 genomes]
rs72823516	0.87[ASN][1000 genomes]
rs7371700	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs908545	0.84[CHB][hapmap]
rs9308674	0.86[ASN][1000 genomes]
rs9308675	0.87[ASN][1000 genomes]
rs9308676	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1010106	chr2:113394981-113556071	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6542074	IL1A	cis	cerebellum	SCAN
rs6542074	PSD4	cis	lymphoblastoid	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113419600-113431200	Weak transcription	Aorta	Aorta
2	chr2:113420800-113431200	Weak transcription	Primary B cells from cord blood	blood
3	chr2:113421200-113431400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:113421400-113448400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:113421600-113438400	Weak transcription	Psoas Muscle	Psoas
6	chr2:113422200-113432000	Weak transcription	Left Ventricle	heart
7	chr2:113422600-113431600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr2:113422600-113432000	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:113422800-113431400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:113422800-113437000	Weak transcription	HMEC	breast
11	chr2:113422800-113438200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:113423000-113429800	Weak transcription	NHEK	skin
13	chr2:113423000-113430000	Weak transcription	NHDF-Ad	bronchial
14	chr2:113423000-113430800	Weak transcription	Fetal Brain Female	brain
15	chr2:113423200-113431400	Weak transcription	Adipose Nuclei	Adipose
16	chr2:113423200-113431400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr2:113423200-113431400	Weak transcription	Spleen	Spleen
18	chr2:113423200-113432200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:113423200-113432200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:113423200-113432400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:113423200-113437000	Weak transcription	Lung	lung
22	chr2:113423200-113445000	Weak transcription	Fetal Brain Male	brain
23	chr2:113423400-113430000	Weak transcription	Thymus	Thymus
24	chr2:113423400-113432000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:113423400-113437000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:113423400-113448400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:113423800-113431400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr2:113423800-113432000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:113424400-113432000	Weak transcription	Placenta	Placenta
30	chr2:113424800-113431200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:113425400-113434200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:113426200-113430600	Enhancers	Liver	Liver
33	chr2:113427000-113429800	Enhancers	HUVEC	blood vessel
34	chr2:113428000-113431200	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr2:113428200-113430000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:113428200-113430000	Enhancers	K562	blood
37	chr2:113428400-113429800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr2:113428400-113436800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:113428600-113430000	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr2:113428600-113430200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:113428600-113430400	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr2:113428600-113432000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr2:113429200-113429800	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr2:113429200-113429800	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr2:113429200-113430000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:113429200-113430000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:113429400-113429800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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