Variant report

Variant	rs7528202
Chromosome Location	chr1:247470187-247470188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247467380..247471480-chr1:247472464..247476921,4	K562	blood:
2	chr1:247461556..247465350-chr1:247467126..247471967,7	K562	blood:
3	chr1:247469630..247471480-chr1:247475421..247477834,2	K562	blood:

Variant related genes	Relation type
ENSG00000162714	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10754542	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10754544	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs10924983	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10924985	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10924989	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs11578583	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1192830	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1192831	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1192832	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12035515	0.87[ASN][1000 genomes]
rs1204493	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1341173	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1616299	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1771929	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1771943	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1771948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778544	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1778546	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1778549	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2153631	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2799540	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3850824	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4320815	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925532	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925533	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925534	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4925621	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56037169	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56399534	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674425	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6692645	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74163745	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7418221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7552292	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs875883	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9426180	1.00[CEU][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9426181	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426233	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9725334	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.98[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	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
3	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
5	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7528202	EFCAB2	cis	parietal	SCAN
rs7528202	OR2T11	cis	parietal	SCAN
rs7528202	ZNF496	cis	Nerve Tibial	GTEx
rs7528202	MAP1LC3C	cis	parietal	SCAN
rs7528202	ZNF496	cis	Thyroid	GTEx
rs7528202	ZNF496	cis	cerebellum	SCAN
rs7528202	ZNF496	cis	Esophagus Muscularis	GTEx
rs7528202	EDIL3	trans	lymphoblastoid	RTeQTL
rs7528202	ZNF496	cis	lung	GTEx
rs7528202	ZNF496	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247455000-247470400	Weak transcription	Fetal Brain Male	brain
2	chr1:247456000-247493400	Weak transcription	Right Atrium	heart
3	chr1:247456600-247471400	Weak transcription	Fetal Heart	heart
4	chr1:247459800-247485800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:247460400-247493400	Strong transcription	Fetal Muscle Leg	muscle
6	chr1:247460800-247471600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:247460800-247474200	Strong transcription	Brain Germinal Matrix	brain
8	chr1:247460800-247474800	Strong transcription	Brain Cingulate Gyrus	brain
9	chr1:247460800-247476200	Weak transcription	HMEC	breast
10	chr1:247460800-247479800	Strong transcription	Fetal Brain Female	brain
11	chr1:247460800-247481000	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:247460800-247491800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:247460800-247493400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr1:247461000-247475400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:247461000-247485400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr1:247461200-247473600	Weak transcription	HUVEC	blood vessel
17	chr1:247461200-247485400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:247461200-247488200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:247461400-247471600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr1:247461400-247485400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:247461400-247493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:247461600-247475200	Strong transcription	Aorta	Aorta
23	chr1:247461600-247481000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:247461800-247474200	Strong transcription	Stomach Smooth Muscle	stomach
25	chr1:247462000-247473800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:247462000-247473800	Strong transcription	Primary T cells from cord blood	blood
27	chr1:247462000-247474000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:247462000-247474000	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr1:247462200-247473800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:247462200-247473800	Strong transcription	K562	blood
31	chr1:247462200-247480000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:247462400-247471000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:247462400-247473800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr1:247462400-247474000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:247462400-247474400	Strong transcription	Dnd41	blood
36	chr1:247462400-247475600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:247462600-247470800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr1:247462600-247474000	Strong transcription	Fetal Intestine Small	intestine
39	chr1:247462600-247479200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:247462800-247473400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:247462800-247488000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:247463000-247470400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr1:247463000-247473400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr1:247463000-247474000	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr1:247463000-247475000	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr1:247463000-247477000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:247463000-247486200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:247463000-247486400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:247463000-247493600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:247463200-247473400	Strong transcription	Placenta	Placenta

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