Variant report

Variant	rs7518984
Chromosome Location	chr1:113463853-113463854
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113454752..113456463-chr1:113462792..113464691,2	K562	blood:
2	chr1:113453716..113456463-chr1:113462131..113464691,2	K562	blood:
3	chr1:113461479..113463865-chr1:113497909..113499529,2	MCF-7	breast:
4	chr1:113461252..113464247-chr1:113498453..113500484,2	K562	blood:
5	chr1:113460022..113462816-chr1:113462818..113464449,2	K562	blood:
6	chr1:113459369..113469193-chr1:113493855..113500263,12	K562	blood:

Variant related genes	Relation type
ENSG00000155380	Chromatin interaction
ENSG00000226419	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11102560	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12064292	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126192	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1216537	0.81[CEU][hapmap]
rs17440299	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442872	1.00[CHD][hapmap]
rs17493313	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17494145	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs17494180	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs1936311	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2149036	1.00[CEU][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28556822	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3849174	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][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]
rs4838971	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839270	1.00[CEU][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839272	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes]
rs4839276	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs55768060	0.84[EUR][1000 genomes]
rs55982206	0.87[EUR][1000 genomes]
rs55992320	0.98[EUR][1000 genomes]
rs56007797	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56019044	0.88[EUR][1000 genomes]
rs56220197	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6676446	0.91[EUR][1000 genomes]
rs6676864	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66899043	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72683432	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683434	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683442	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72683453	0.94[EUR][1000 genomes]
rs72683454	0.96[EUR][1000 genomes]
rs72683459	0.87[EUR][1000 genomes]
rs7524567	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7536532	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][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]
rs7540321	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7542229	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7545602	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548109	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7550843	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7552903	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9429505	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][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]
rs9429709	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429710	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
10	esv3399982	chr1:113358580-113542255	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
11	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
12	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
13	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7518984	SLC16A1	Cis_1M	lymphoblastoid	RTeQTL
rs7518984	OVGP1	cis	cerebellum	SCAN
rs7518984	LRIG2	cis	cerebellum	SCAN
rs7518984	DDX20	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113447800-113470200	Weak transcription	Fetal Kidney	kidney
2	chr1:113449000-113465600	Weak transcription	Placenta	Placenta
3	chr1:113449000-113466000	Weak transcription	Esophagus	oesophagus
4	chr1:113449000-113468400	Weak transcription	Lung	lung
5	chr1:113449600-113470000	Weak transcription	Brain Angular Gyrus	brain
6	chr1:113449600-113474600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:113449600-113477200	Weak transcription	Stomach Mucosa	stomach
8	chr1:113449800-113466000	Weak transcription	Brain Anterior Caudate	brain
9	chr1:113450400-113465800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:113450400-113466200	Weak transcription	Gastric	stomach
11	chr1:113451400-113475400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:113452400-113470800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:113452800-113473000	Strong transcription	Dnd41	blood
14	chr1:113452800-113476600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:113455400-113464000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:113455800-113472200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:113456200-113473000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:113456400-113472400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:113456600-113472800	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr1:113458000-113470400	Weak transcription	Fetal Brain Male	brain
21	chr1:113458000-113490600	Weak transcription	Right Atrium	heart
22	chr1:113458200-113466000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:113458200-113473000	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:113458200-113473400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:113458400-113464600	Weak transcription	Right Ventricle	heart
26	chr1:113458400-113473000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:113458400-113473000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:113458600-113467200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:113458600-113478400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:113458800-113465000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:113458800-113468200	Strong transcription	HMEC	breast
32	chr1:113458800-113470000	Weak transcription	NHDF-Ad	bronchial
33	chr1:113458800-113472400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:113458800-113472400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:113459200-113467400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:113459600-113464600	Strong transcription	Hela-S3	cervix
37	chr1:113459600-113465000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:113460200-113465600	Weak transcription	Colonic Mucosa	Colon
39	chr1:113460200-113466000	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:113460200-113466400	Weak transcription	NHLF	lung
41	chr1:113460200-113468800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr1:113460200-113470000	Weak transcription	Primary B cells from cord blood	blood
43	chr1:113460200-113475400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr1:113460400-113466000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:113460400-113466000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:113460400-113466000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:113460400-113467800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:113460400-113472400	Weak transcription	Small Intestine	intestine
49	chr1:113460400-113479800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:113460400-113481000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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