Variant report

Variant	rs10184457
Chromosome Location	chr2:98579729-98579730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98578999..98581237-chr2:98611581..98614164,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10167772	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10168543	0.82[AFR][1000 genomes]
rs10168709	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10169155	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10175129	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10176826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180434	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10180837	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10183768	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10184393	0.81[ASN][1000 genomes]
rs10184552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10188497	0.82[AFR][1000 genomes]
rs10188713	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10189414	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10191101	0.85[CHB][hapmap]
rs10192322	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs10206684	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10208070	0.85[EUR][1000 genomes]
rs10209970	0.85[CHB][hapmap]
rs10210299	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210880	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1024086	0.85[CHB][hapmap]
rs11893437	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11894541	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11895170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897301	0.83[AFR][1000 genomes]
rs12712147	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12712162	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12712163	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12712172	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12992955	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13000585	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13008678	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13008904	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13009300	1.00[ASN][1000 genomes]
rs13012645	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13387725	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13404788	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13427422	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1446327	0.83[AFR][1000 genomes]
rs1503202	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1960329	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs1982336	0.94[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs2121271	0.85[CHB][hapmap]
rs2293679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35203092	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs35402416	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35776557	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs35807655	0.83[EUR][1000 genomes]
rs35940587	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36079497	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3821053	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs55817781	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6707750	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6712078	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6713504	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718982	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6721323	0.94[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs6721467	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751727	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6756969	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs718159	0.81[AFR][1000 genomes]
rs7557495	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7578638	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7588227	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7591374	0.89[ASN][1000 genomes]
rs7594928	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7595039	0.83[AFR][1000 genomes]
rs7599043	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7605288	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9784011	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9808558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats 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	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10184457	LONRF2	cis	parietal	SCAN
rs10184457	INPP4A	cis	cerebellum	SCAN
rs10184457	TEKT4	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98563600-98589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:98564600-98580600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:98567600-98586600	Weak transcription	Fetal Stomach	stomach
4	chr2:98568000-98583000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:98568200-98580800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr2:98568200-98599200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:98568400-98586600	Weak transcription	Aorta	Aorta
8	chr2:98568400-98592000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:98569200-98580600	Weak transcription	NHDF-Ad	bronchial
10	chr2:98569200-98581400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr2:98571000-98586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:98574200-98580400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:98574400-98586200	Weak transcription	NH-A	brain
14	chr2:98574600-98582200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:98574600-98583200	Weak transcription	Primary B cells from cord blood	blood
16	chr2:98574600-98583400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:98574800-98585200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:98574800-98586200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:98575000-98583000	Weak transcription	Gastric	stomach
20	chr2:98575000-98585000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:98575000-98586800	Weak transcription	Brain Angular Gyrus	brain
22	chr2:98575000-98589000	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:98575200-98580600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:98575200-98580600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:98575200-98583000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:98575200-98583200	Weak transcription	Small Intestine	intestine
27	chr2:98575200-98584400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:98575200-98592600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:98575400-98581400	Weak transcription	Left Ventricle	heart
30	chr2:98575400-98583200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:98575400-98583400	Weak transcription	Spleen	Spleen
32	chr2:98575400-98585000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:98575400-98595000	Weak transcription	HSMM	muscle
34	chr2:98575600-98586600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:98575600-98586600	Weak transcription	Lung	lung
36	chr2:98575800-98580400	Weak transcription	Ovary	ovary
37	chr2:98575800-98582600	Weak transcription	Right Atrium	heart
38	chr2:98575800-98587600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:98576000-98582000	Weak transcription	Psoas Muscle	Psoas
40	chr2:98576000-98584400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:98577200-98580000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:98578200-98580800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr2:98578200-98584200	Weak transcription	Brain Substantia Nigra	brain
44	chr2:98578400-98584200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:98578400-98586600	Weak transcription	Brain Anterior Caudate	brain
46	chr2:98578400-98587200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:98579000-98579800	Flanking Active TSS	GM12878-XiMat	blood
48	chr2:98579000-98581000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:98579000-98581000	Enhancers	NHEK	skin
50	chr2:98579000-98582000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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