Variant report

Variant	rs1778549
Chromosome Location	chr1:247476616-247476617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247473800..247482682-chr1:247490121..247498423,19	K562	blood:
2	chr1:247456054..247458907-chr1:247476595..247478143,2	K562	blood:
3	chr1:247467380..247471480-chr1:247472464..247476921,4	K562	blood:

Variant related genes	Relation type
ENSG00000202079	Chromatin interaction
ENSG00000162714	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10754542	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10754544	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10924983	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10924985	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10924989	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs11578583	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1192830	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1192831	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[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];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12035515	0.88[ASN][1000 genomes]
rs1204493	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1341173	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1616299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1771929	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1771943	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1771948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778544	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1778546	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2153631	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2799540	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3850824	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4320815	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925532	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925533	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925534	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4925621	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56037169	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56399534	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6674425	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6692645	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7418221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7528202	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]
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];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7552292	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs875883	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9426180	1.00[CEU][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9426181	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9426182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9426233	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9725334	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.97[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	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	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
3	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
4	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
rs1778549	ZNF496	cis	lung	GTEx
rs1778549	EFCAB2	cis	parietal	SCAN
rs1778549	OR2T11	cis	parietal	SCAN
rs1778549	ZNF496	cis	Nerve Tibial	GTEx
rs1778549	ZNF496	cis	Esophagus Muscularis	GTEx
rs1778549	MAP1LC3C	cis	parietal	SCAN
rs1778549	ZNF496	cis	parietal	SCAN
rs1778549	EDIL3	trans	lymphoblastoid	RTeQTL
rs1778549	ZNF496	cis	Thyroid	GTEx
rs1778549	ZNF496	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247456000-247493400	Weak transcription	Right Atrium	heart
2	chr1:247459800-247485800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:247460400-247493400	Strong transcription	Fetal Muscle Leg	muscle
4	chr1:247460800-247479800	Strong transcription	Fetal Brain Female	brain
5	chr1:247460800-247481000	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:247460800-247491800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:247460800-247493400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:247461000-247485400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:247461200-247485400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:247461200-247488200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:247461400-247485400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:247461400-247493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:247461600-247481000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:247462200-247480000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:247462600-247479200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:247462800-247488000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:247463000-247477000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:247463000-247486200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:247463000-247486400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:247463000-247493600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:247463200-247481000	Strong transcription	Left Ventricle	heart
22	chr1:247463200-247493400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:247463400-247486000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:247463400-247486600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:247464600-247479600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:247464600-247486000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:247464800-247493400	Strong transcription	Fetal Stomach	stomach
28	chr1:247465200-247493400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:247466800-247485600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr1:247467600-247493800	Weak transcription	Stomach Mucosa	stomach
31	chr1:247468400-247494000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:247469000-247493600	Weak transcription	Psoas Muscle	Psoas
33	chr1:247469400-247478600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:247469400-247493800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:247471200-247485600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:247471800-247478800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:247471800-247480400	Weak transcription	GM12878-XiMat	blood
38	chr1:247471800-247493400	Weak transcription	Fetal Heart	heart
39	chr1:247472400-247478600	Weak transcription	NHDF-Ad	bronchial
40	chr1:247472400-247483600	Weak transcription	Fetal Brain Male	brain
41	chr1:247472600-247484400	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:247472800-247478600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:247472800-247478600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:247472800-247482800	Weak transcription	Fetal Kidney	kidney
45	chr1:247472800-247493400	Weak transcription	Small Intestine	intestine
46	chr1:247473000-247485400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:247473000-247485600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:247473400-247476800	Weak transcription	Placenta	Placenta
49	chr1:247473400-247480800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:247473400-247483600	Weak transcription	Rectal Mucosa Donor 29	rectum

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