Variant report

Variant	rs4970998
Chromosome Location	chr1:151091181-151091182
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151089435..151091250-chr1:151117616..151120097,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143434	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10788798	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10788799	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10788800	0.81[ASN][1000 genomes]
rs11204777	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204778	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204780	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204782	1.00[JPT][hapmap]
rs11807526	1.00[JPT][hapmap]
rs12039334	0.82[EUR][1000 genomes]
rs12039542	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12087892	1.00[JPT][hapmap]
rs12117163	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12569193	0.86[JPT][hapmap]
rs1524773	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2067606	1.00[JPT][hapmap]
rs2140709	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2902810	0.94[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[LWK][hapmap];0.84[MKK][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs3738481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3806386	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs3806387	0.89[CEU][hapmap];0.88[CHB][hapmap];0.83[EUR][1000 genomes]
rs4357530	0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs4512652	0.86[JPT][hapmap]
rs4970939	0.87[EUR][1000 genomes]
rs4970941	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4970993	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4970999	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971000	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4971002	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971003	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971005	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971006	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971007	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971008	0.84[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5023311	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61819219	0.81[ASN][1000 genomes]
rs6587552	0.81[CHD][hapmap]
rs6587553	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs6587557	0.86[JPT][hapmap]
rs6656450	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6668894	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6674970	0.86[JPT][hapmap]
rs6676190	0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6694158	1.00[CHB][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap]
rs7523731	1.00[JPT][hapmap]
rs7532312	1.00[CHB][hapmap]
rs7540258	1.00[CHB][hapmap]
rs7550434	1.00[CHB][hapmap]
rs7554936	1.00[JPT][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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv872421	chr1:151055670-151098077	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4970998	BNIPL	cis	Thyroid	GTEx
rs4970998	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs4970998	CDC42SE1	cis	lymphoblastoid	seeQTL
rs4970998	BNIPL	cis	lung	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151044400-151103600	Weak transcription	Small Intestine	intestine
2	chr1:151044800-151098800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:151052200-151103000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:151061800-151105600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:151064200-151103400	Weak transcription	Colonic Mucosa	Colon
6	chr1:151067000-151103400	Weak transcription	Fetal Brain Male	brain
7	chr1:151072400-151091400	Weak transcription	Fetal Lung	lung
8	chr1:151074000-151101000	Weak transcription	Fetal Heart	heart
9	chr1:151078000-151096400	Strong transcription	Fetal Intestine Small	intestine
10	chr1:151079200-151093800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:151079600-151091400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:151079600-151096400	Weak transcription	Hela-S3	cervix
13	chr1:151079800-151091600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:151079800-151097000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:151079800-151102000	Weak transcription	NHDF-Ad	bronchial
16	chr1:151079800-151103400	Weak transcription	NH-A	brain
17	chr1:151079800-151103400	Weak transcription	NHEK	skin
18	chr1:151079800-151103400	Weak transcription	NHLF	lung
19	chr1:151079800-151106200	Weak transcription	HSMMtube	muscle
20	chr1:151079800-151114800	Weak transcription	HSMM	muscle
21	chr1:151081000-151100800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:151081200-151095000	Weak transcription	Aorta	Aorta
23	chr1:151081200-151102000	Weak transcription	Brain Germinal Matrix	brain
24	chr1:151081200-151103400	Weak transcription	GM12878-XiMat	blood
25	chr1:151081400-151103000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:151081600-151097000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:151081800-151097400	Weak transcription	Stomach Mucosa	stomach
28	chr1:151081800-151103000	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:151083400-151103600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:151085000-151092600	Strong transcription	Fetal Thymus	thymus
31	chr1:151085000-151093800	Strong transcription	Thymus	Thymus
32	chr1:151085800-151103200	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:151086200-151092000	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:151086400-151091800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr1:151086400-151093000	Strong transcription	Fetal Stomach	stomach
36	chr1:151087000-151103600	Weak transcription	Psoas Muscle	Psoas
37	chr1:151087400-151091600	Strong transcription	Primary T cells from cord blood	blood
38	chr1:151087600-151091800	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:151088200-151097200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:151088400-151092000	Strong transcription	Fetal Intestine Large	intestine
41	chr1:151088400-151095200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:151088800-151091800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:151089000-151095400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:151089200-151091800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:151089200-151091800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:151089200-151091800	Strong transcription	Fetal Muscle Trunk	muscle
47	chr1:151089200-151091800	Strong transcription	Placenta	Placenta
48	chr1:151089200-151092000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:151089200-151092000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr1:151089200-151098000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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