Variant report

Variant	rs4493873
Chromosome Location	chr8:92075643-92075644
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:92060898..92063095-chr8:92075458..92078232,3	MCF-7	breast:
2	chr8:92051480..92053113-chr8:92073379..92075830,2	K562	blood:
3	chr8:92072209..92075764-chr8:92075998..92078748,4	MCF-7	breast:
4	chr8:92063513..92065129-chr8:92073946..92075956,2	MCF-7	breast:
5	chr8:91995287..91997853-chr8:92074823..92077040,2	K562	blood:
6	chr8:92054872..92056840-chr8:92073842..92076299,2	K562	blood:
7	chr8:92050768..92053463-chr8:92074027..92075794,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253250	Chromatin interaction
ENSG00000155099	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10087552	0.86[CHB][hapmap]
rs10090581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10093786	0.86[CHB][hapmap]
rs10095065	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10095630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10096149	0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs10097502	0.86[CHB][hapmap]
rs10100069	0.85[EUR][1000 genomes]
rs10110267	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10216413	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10942	0.88[CEU][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10956790	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10956791	0.88[EUR][1000 genomes]
rs10956792	0.95[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs10956793	0.88[EUR][1000 genomes]
rs10956794	0.93[GIH][hapmap]
rs10956795	0.86[GIH][hapmap]
rs10956796	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1138489	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11557571	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11778758	0.93[GIH][hapmap]
rs11785003	0.93[GIH][hapmap]
rs11786324	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1180	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11992004	0.85[CHB][hapmap]
rs12334996	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12542178	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12542580	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12545969	0.88[EUR][1000 genomes]
rs12546650	0.91[GIH][hapmap]
rs12679861	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13280667	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs28372564	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28429767	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28629349	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28750250	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35066004	0.82[CHD][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap]
rs3808378	0.82[CHD][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3885969	0.93[GIH][hapmap]
rs4128119	0.85[GIH][hapmap]
rs4129720	0.82[CHD][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap]
rs4259381	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4338063	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs4339600	0.86[CHB][hapmap]
rs4360257	0.81[CHB][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap]
rs4373488	0.82[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4374950	0.85[CHB][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap]
rs4392858	0.85[CHB][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap]
rs4419777	0.88[GIH][hapmap]
rs4419778	0.86[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap]
rs4446697	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4501547	0.81[CHB][hapmap];0.86[GIH][hapmap]
rs4501548	0.98[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4501550	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4501551	0.83[GIH][hapmap]
rs4504594	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4515507	0.86[CHB][hapmap]
rs4568579	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4577919	0.93[GIH][hapmap]
rs4596614	0.83[GIH][hapmap]
rs4620242	0.93[GIH][hapmap]
rs4637780	0.86[CHB][hapmap]
rs55775840	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56084507	0.91[EUR][1000 genomes]
rs56278134	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56306245	0.85[EUR][1000 genomes]
rs57987672	0.82[ASN][1000 genomes]
rs58278856	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6471265	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6471268	0.90[GIH][hapmap]
rs6471269	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs6471270	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs6471271	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs6987764	0.83[GIH][hapmap]
rs6993713	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7009170	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs7009178	0.80[ASN][1000 genomes]
rs7010715	0.86[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap]
rs7014578	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7015294	0.86[CHB][hapmap];0.86[GIH][hapmap]
rs7815938	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7816107	0.82[EUR][1000 genomes]
rs7819178	0.82[EUR][1000 genomes]
rs7820904	0.95[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7821050	0.86[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap]
rs7822774	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7822807	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7823844	0.90[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap]
rs7832313	0.86[CHB][hapmap]
rs7832592	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7832896	0.86[CHB][hapmap]
rs7841266	0.85[EUR][1000 genomes]
rs7842678	0.86[CHB][hapmap];0.86[GIH][hapmap]
rs7843665	0.81[ASN][1000 genomes]
rs7844122	0.86[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap]
rs7844277	0.80[ASN][1000 genomes]
rs7845508	0.86[CHB][hapmap]
rs7846033	0.91[CHB][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs8081	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9643319	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9918929	0.82[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9987161	0.84[CHB][hapmap]

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	nsv1028628	chr8:91680968-92418954	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv539672	chr8:91680968-92418954	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv2758623	chr8:91974499-92273724	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2759629	chr8:91974499-92273724	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers 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	26 gene(s)	inside rSNPs	diseases
5	nsv831390	chr8:92037011-92198605	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Migraine - clinic-based	23793025	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4493873	RUNX1T1	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:92053800-92080400	Weak transcription	Fetal Brain Female	brain
2	chr8:92061000-92079200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr8:92061400-92076600	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr8:92063200-92079000	Weak transcription	Primary B cells from cord blood	blood
5	chr8:92066000-92078000	Weak transcription	K562	blood
6	chr8:92066200-92081400	Weak transcription	Left Ventricle	heart
7	chr8:92068400-92077400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr8:92070400-92078600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr8:92070600-92079200	Weak transcription	Fetal Intestine Large	intestine
10	chr8:92070600-92080600	Weak transcription	Colon Smooth Muscle	Colon
11	chr8:92070600-92081200	Weak transcription	Aorta	Aorta
12	chr8:92070800-92080600	Weak transcription	Fetal Kidney	kidney
13	chr8:92071000-92076800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr8:92071400-92079200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr8:92071400-92080800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr8:92071600-92077400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr8:92071600-92079200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr8:92071800-92079200	Weak transcription	Brain Anterior Caudate	brain
19	chr8:92071800-92080400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr8:92072000-92080400	Weak transcription	NHEK	skin
21	chr8:92072200-92079400	Weak transcription	A549	lung
22	chr8:92072400-92078000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr8:92072400-92080600	Weak transcription	NH-A	brain
24	chr8:92072400-92081800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr8:92073000-92077800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr8:92073000-92077800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr8:92073000-92079000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr8:92073000-92080200	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr8:92073000-92080600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr8:92073000-92080800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr8:92073200-92079000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr8:92073200-92079200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr8:92073200-92080600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr8:92073200-92081200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr8:92073200-92081200	Weak transcription	Fetal Thymus	thymus
36	chr8:92073400-92079200	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr8:92073400-92080000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr8:92073400-92080600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr8:92073400-92081200	Weak transcription	Ovary	ovary
40	chr8:92073600-92079000	Weak transcription	GM12878-XiMat	blood
41	chr8:92073600-92079200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr8:92073600-92080000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr8:92073800-92076400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr8:92073800-92079200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr8:92073800-92079200	Weak transcription	HSMM	muscle
46	chr8:92073800-92081200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr8:92074000-92078000	Weak transcription	Small Intestine	intestine
48	chr8:92074400-92077400	Weak transcription	Adipose Nuclei	Adipose
49	chr8:92074400-92078400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr8:92074600-92076200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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