Variant report

Variant	rs998199
Chromosome Location	chr1:45912898-45912899
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45911582..45914439-chr1:45956786..45959560,2	MCF-7	breast:
2	chr1:45185686..45188645-chr1:45911904..45916930,4	K562	blood:

Variant related genes	Relation type
ENSG00000070759	Chromatin interaction
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10789463	0.96[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10789465	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10890328	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10890329	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10890331	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211109	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211122	0.94[ASN][1000 genomes]
rs11211129	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11211130	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11580609	0.91[CHB][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12119202	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12133294	0.81[AMR][1000 genomes]
rs12139364	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12568144	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12729715	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12738318	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743512	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.94[ASN][1000 genomes]
rs1765709	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2036021	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2275276	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2356413	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2492841	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4660859	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4660861	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4660869	0.81[AMR][1000 genomes]
rs512026	0.91[CHB][hapmap]
rs518365	0.86[CHB][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs6657237	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6661321	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs71500084	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs781058	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs781226	0.81[CHD][hapmap]
rs781232	0.81[CHD][hapmap]
rs7903	0.91[CHB][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs937291	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
6	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
7	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
8	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
9	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs998199	AKR1A1	cis	multi-tissue	Pritchard
rs998199	CCDC163P	cis	Stomach	GTEx
rs998199	CCDC163P	cis	Nerve Tibial	GTEx
rs998199	CCDC163P	cis	Whole Blood	GTEx
rs998199	CCDC163P	cis	Artery Tibial	GTEx
rs998199	Hs.396207	cis	multi-tissue	Pritchard
rs998199	GPBP1L1	cis	Lymphoblastoid	GTEx
rs998199	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs998199	CCDC163P	cis	Muscle Skeletal	GTEx
rs998199	CCDC163P	cis	lung	GTEx
rs998199	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs998199	CCDC163P	cis	Esophagus Muscularis	GTEx
rs998199	CCDC163P	cis	Thyroid	GTEx
rs998199	MUTYH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45888200-45920600	Weak transcription	Primary B cells from cord blood	blood
2	chr1:45889800-45940600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:45902600-45924200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:45903200-45920600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr1:45905200-45921000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr1:45907000-45919600	Weak transcription	Primary T cells from cord blood	blood
7	chr1:45908600-45920600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:45908600-45920600	Weak transcription	Brain Substantia Nigra	brain
9	chr1:45909000-45924600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:45909200-45922400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:45910600-45920200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:45911000-45918200	Weak transcription	Fetal Intestine Small	intestine
13	chr1:45911000-45930400	Weak transcription	Psoas Muscle	Psoas
14	chr1:45911400-45924400	Weak transcription	Placenta	Placenta
15	chr1:45911600-45914800	Enhancers	K562	blood
16	chr1:45912200-45918800	Weak transcription	Gastric	stomach
17	chr1:45912600-45913000	Enhancers	Ovary	ovary
18	chr1:45912800-45922400	Weak transcription	Liver	Liver
19	chr1:45912800-45923800	Weak transcription	HepG2	liver

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