Variant report

Variant	rs16847633
Chromosome Location	chr1:174935508-174935509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174845147..174847335-chr1:174934158..174936511,2	K562	blood:
2	chr1:174934109..174936598-chr1:174962086..174965917,3	MCF-7	breast:
3	chr1:174934157..174936495-chr1:174950544..174953349,2	K562	blood:
4	chr1:174934516..174936659-chr1:174945520..174947584,2	MCF-7	breast:
5	chr1:174933583..174936463-chr1:174967523..174970706,3	MCF-7	breast:
6	chr1:174927580..174945830-chr1:174955726..174971213,32	K562	blood:

Variant related genes	Relation type
ENSG00000152061	Chromatin interaction
ENSG00000116161	Chromatin interaction
ENSG00000252552	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1002125	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489333	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912849	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10912850	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10912870	0.84[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12065854	0.92[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12066247	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12067259	0.85[LWK][hapmap]
rs12068100	0.88[AFR][1000 genomes]
rs12068637	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12069057	0.85[LWK][hapmap]
rs12073786	0.88[AFR][1000 genomes]
rs12074821	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12087196	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12087589	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12088588	0.81[ASN][1000 genomes]
rs12562194	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12565944	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12566477	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16847450	0.92[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs16847563	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes]
rs16847576	0.85[LWK][hapmap]
rs16847706	1.00[ASW][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2285209	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28660133	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41266068	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41266072	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57366106	0.82[AMR][1000 genomes]
rs61828087	0.81[AMR][1000 genomes]
rs61828088	0.81[AMR][1000 genomes]
rs61828117	0.90[AMR][1000 genomes]
rs61828121	0.87[AMR][1000 genomes]
rs61828143	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61828144	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61828148	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61828149	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61828151	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61828152	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61828156	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61828157	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6658861	0.80[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16847633	DARS2	cis	cerebellum	SCAN
rs16847633	LOC646870	cis	parietal	SCAN
rs16847633	SLC9A11	cis	parietal	SCAN
rs16847633	PRDX6	cis	parietal	SCAN
rs16847633	RABGAP1L	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174874200-174938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:174910800-174957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:174924000-174938200	Weak transcription	Psoas Muscle	Psoas
4	chr1:174924200-174967800	Weak transcription	Brain Germinal Matrix	brain
5	chr1:174924400-174958200	Weak transcription	Fetal Brain Male	brain
6	chr1:174925000-174940800	Weak transcription	Gastric	stomach
7	chr1:174928000-174938200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:174930800-174937800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:174932000-174938400	Enhancers	Fetal Intestine Small	intestine
10	chr1:174932400-174936600	Enhancers	Fetal Lung	lung
11	chr1:174932600-174941600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:174932800-174937000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr1:174932800-174937600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:174932800-174938400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr1:174932800-174939000	Enhancers	Fetal Intestine Large	intestine
16	chr1:174933000-174936000	Enhancers	Brain Anterior Caudate	brain
17	chr1:174933000-174953600	Weak transcription	Fetal Heart	heart
18	chr1:174933200-174935800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr1:174933200-174936000	Enhancers	NHEK	skin
20	chr1:174933400-174935600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:174933400-174935600	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr1:174933400-174936000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:174933400-174937600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr1:174933600-174935600	Enhancers	Brain Hippocampus Middle	brain
25	chr1:174933600-174935800	Enhancers	Fetal Kidney	kidney
26	chr1:174933600-174935800	Flanking Active TSS	HSMMtube	muscle
27	chr1:174933600-174936000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:174933600-174936000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr1:174933600-174936000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr1:174933600-174936000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr1:174933600-174936000	Enhancers	Brain Substantia Nigra	brain
32	chr1:174933600-174936200	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr1:174933600-174938800	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr1:174933800-174936000	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr1:174933800-174936200	Weak transcription	HUVEC	blood vessel
36	chr1:174933800-174937200	Weak transcription	A549	lung
37	chr1:174934000-174936000	Flanking Active TSS	Dnd41	blood
38	chr1:174934000-174937400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:174934000-174938200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:174934200-174936000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr1:174934200-174936000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:174934200-174936000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr1:174934200-174937200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr1:174934400-174935600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:174934600-174935600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:174934600-174943800	Weak transcription	Pancreas	Pancrea
47	chr1:174934800-174937000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:174934800-174937600	Enhancers	Liver	Liver
49	chr1:174934800-174940400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:174934800-174943800	Weak transcription	Aorta	Aorta

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