Variant report

Variant	rs12097043
Chromosome Location	chr1:153732973-153732974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153697814..153700454-chr1:153732023..153734328,2	K562	blood:
2	chr1:153721928..153724175-chr1:153731100..153734049,2	MCF-7	breast:
3	chr1:153732136..153734221-chr1:153747059..153748574,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199565	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000243613	Chromatin interaction
ENSG00000143624	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10082235	1.00[CHB][hapmap]
rs11264299	0.94[EUR][1000 genomes]
rs11264336	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1132619	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12062022	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12068901	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070179	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070559	0.94[EUR][1000 genomes]
rs12071801	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076697	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12097583	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34527123	1.00[ASN][1000 genomes]
rs36064263	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3891075	1.00[CHB][hapmap]
rs4073768	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41265191	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55658698	0.94[EUR][1000 genomes]
rs55778008	0.94[EUR][1000 genomes]
rs56167936	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56910871	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57314764	0.83[EUR][1000 genomes]
rs60100741	0.84[EUR][1000 genomes]
rs60316596	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60827720	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803563	0.94[EUR][1000 genomes]
rs61803565	0.94[EUR][1000 genomes]
rs61803566	0.88[EUR][1000 genomes]
rs61803567	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61803571	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61803573	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61803652	1.00[ASN][1000 genomes]
rs6427085	0.90[EUR][1000 genomes]
rs6660232	0.84[EUR][1000 genomes]
rs6663011	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6663988	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6668229	0.83[EUR][1000 genomes]
rs6672371	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6682411	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6687602	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6689176	0.94[EUR][1000 genomes]
rs6692298	1.00[CHB][hapmap]
rs74115713	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512561	0.84[EUR][1000 genomes]
rs7515716	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7520045	0.84[EUR][1000 genomes]
rs7520235	0.83[EUR][1000 genomes]
rs7533987	1.00[CHB][hapmap]
rs7536700	1.00[CHB][hapmap]
rs7543790	1.00[CHB][hapmap]
rs7556155	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7556379	0.84[EUR][1000 genomes]
rs7556575	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
4	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12097043	S100A13	cis	lymphoblastoid	seeQTL
rs12097043	SLC27A3	cis	lymphoblastoid	seeQTL
rs12097043	SLC27A3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153711400-153735600	Strong transcription	Fetal Muscle Leg	muscle
2	chr1:153712600-153741400	Strong transcription	Placenta	Placenta
3	chr1:153712800-153737800	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr1:153712800-153737800	Strong transcription	Placenta Amnion	Placenta Amnion
5	chr1:153712800-153738000	Strong transcription	Fetal Brain Female	brain
6	chr1:153712800-153738200	Strong transcription	Thymus	Thymus
7	chr1:153712800-153742800	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:153712800-153743200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:153712800-153744800	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:153712800-153746400	Strong transcription	Brain Germinal Matrix	brain
11	chr1:153712800-153751800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:153713000-153734800	Strong transcription	Spleen	Spleen
13	chr1:153713000-153735200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:153713000-153738200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:153713000-153738600	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:153713000-153745400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:153713000-153745400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:153713000-153746400	Strong transcription	Primary T cells from cord blood	blood
19	chr1:153713000-153747000	Strong transcription	Dnd41	blood
20	chr1:153714000-153746800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:153715200-153738000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:153715400-153745600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:153715600-153745600	Strong transcription	Fetal Thymus	thymus
24	chr1:153716400-153746000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:153719800-153746800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:153721000-153738200	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr1:153722000-153735400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:153722000-153743800	Strong transcription	Fetal Stomach	stomach
29	chr1:153722200-153738000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:153722200-153742800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr1:153722400-153735200	Strong transcription	Duodenum Mucosa	Duodenum
32	chr1:153722400-153735600	Strong transcription	Brain Hippocampus Middle	brain
33	chr1:153722400-153738200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:153722400-153743000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:153722400-153746200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:153722400-153746800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:153722600-153742800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:153722600-153746600	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr1:153722800-153738200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:153722800-153742800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:153723000-153735400	Strong transcription	Brain Cingulate Gyrus	brain
42	chr1:153723600-153735400	Strong transcription	Brain Anterior Caudate	brain
43	chr1:153723600-153735800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:153723600-153736000	Strong transcription	Colonic Mucosa	Colon
45	chr1:153723600-153746800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:153723800-153735600	Weak transcription	Stomach Mucosa	stomach
47	chr1:153723800-153736600	Strong transcription	Liver	Liver
48	chr1:153723800-153740800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr1:153724000-153736000	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr1:153724000-153738000	Strong transcription	GM12878-XiMat	blood

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