Variant report

Variant	rs1520854
Chromosome Location	chr2:190310982-190310983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190310567..190312254-chr2:190312605..190315190,2	MCF-7	breast:
2	chr2:190310939..190313402-chr2:190419193..190420763,2	MCF-7	breast:
3	chr2:190308951..190311414-chr2:190525622..190528539,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138381	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10166420	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10175108	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10188246	0.80[ASN][1000 genomes]
rs10198663	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10207812	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10210634	0.91[ASN][1000 genomes]
rs10804029	0.86[ASN][1000 genomes]
rs10931417	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11676905	0.80[ASN][1000 genomes]
rs11677167	0.91[ASN][1000 genomes]
rs11678414	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12613903	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12622720	0.91[ASN][1000 genomes]
rs12623394	0.87[ASN][1000 genomes]
rs12693539	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693540	0.91[ASN][1000 genomes]
rs12994482	0.80[ASN][1000 genomes]
rs13009912	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13015207	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13018252	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13035381	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1356976	0.93[ASN][1000 genomes]
rs1520856	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1520858	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs1520866	0.92[ASN][1000 genomes]
rs1595749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16831454	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1851104	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1866605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1898971	0.91[ASN][1000 genomes]
rs1992295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304702	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2351932	0.83[ASN][1000 genomes]
rs2351934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2683012	0.83[ASN][1000 genomes]
rs2882805	0.92[ASN][1000 genomes]
rs4309611	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4580411	0.88[ASN][1000 genomes]
rs4666775	0.96[ASN][1000 genomes]
rs4667280	0.89[ASN][1000 genomes]
rs4667284	0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs6434340	0.88[ASN][1000 genomes]
rs6434342	0.96[ASN][1000 genomes]
rs6434343	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6738193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6752545	0.91[ASN][1000 genomes]
rs734859	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7420765	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7422875	0.80[ASN][1000 genomes]
rs7425383	0.80[ASN][1000 genomes]
rs744556	0.87[ASN][1000 genomes]
rs745742	0.91[ASN][1000 genomes]
rs7556928	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7566093	0.91[ASN][1000 genomes]
rs7574403	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590098	0.88[AMR][1000 genomes]
rs8179541	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8179732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs893407	0.91[ASN][1000 genomes]
rs893408	0.87[ASN][1000 genomes]
rs9677436	0.84[AFR][1000 genomes];0.91[ASN][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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv584062	chr2:190272195-190376493	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1520854	AC013439.4	cis	Muscle Skeletal	GTEx
rs1520854	PKIG	trans	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190306800-190323000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:190306800-190323800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:190306800-190344200	Weak transcription	Esophagus	oesophagus
4	chr2:190307000-190317600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:190307000-190334200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:190307200-190312800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:190307200-190313200	Weak transcription	Fetal Kidney	kidney
8	chr2:190307200-190313400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:190307400-190311800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:190307400-190312200	Weak transcription	Placenta	Placenta
11	chr2:190307400-190312400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:190307400-190312800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr2:190307400-190312800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:190307400-190313000	Weak transcription	HSMMtube	muscle
15	chr2:190307600-190311000	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:190307600-190311400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr2:190307600-190312200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:190307600-190312200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:190307600-190312600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:190307600-190312600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:190307600-190312800	Weak transcription	Brain Anterior Caudate	brain
22	chr2:190307600-190313000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:190307600-190313200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:190307600-190314200	Weak transcription	Brain Germinal Matrix	brain
25	chr2:190307600-190314800	Weak transcription	Left Ventricle	heart
26	chr2:190307600-190314800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:190307600-190315000	Weak transcription	Gastric	stomach
28	chr2:190307600-190316200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:190307600-190316200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:190307600-190316400	Weak transcription	Colonic Mucosa	Colon
31	chr2:190307600-190317000	Weak transcription	Fetal Stomach	stomach
32	chr2:190307600-190317200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr2:190307600-190317400	Weak transcription	Lung	lung
34	chr2:190307600-190322600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:190307600-190323400	Weak transcription	Ovary	ovary
36	chr2:190307600-190330000	Weak transcription	Fetal Heart	heart
37	chr2:190307600-190334200	Weak transcription	Pancreas	Pancrea
38	chr2:190307600-190338200	Weak transcription	Spleen	Spleen
39	chr2:190307600-190342000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:190307600-190342600	Weak transcription	Aorta	Aorta
41	chr2:190307800-190311000	Weak transcription	NH-A	brain
42	chr2:190307800-190311200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr2:190307800-190312000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:190307800-190313000	Weak transcription	Brain Substantia Nigra	brain
45	chr2:190307800-190314000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr2:190307800-190332400	Weak transcription	Stomach Mucosa	stomach
47	chr2:190308000-190311800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr2:190308000-190312800	Weak transcription	Fetal Thymus	thymus
49	chr2:190308000-190313000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:190308000-190313200	Weak transcription	Brain Hippocampus Middle	brain

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