Variant report

Variant	rs2864871
Chromosome Location	chr1:150766964-150766965
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	chr1:150761240..150763209-chr1:150766177..150768567,2	MCF-7	breast:
2	chr1:150766703..150768461-chr1:150769948..150772037,2	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1027699	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10305664	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10305672	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10305673	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10305704	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10305711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10305714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10788792	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs10788794	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10888391	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10888392	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10888393	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10888394	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10888395	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10888397	0.80[EUR][1000 genomes]
rs11204691	0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap]
rs11204697	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs11204698	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs11204704	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs11204722	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11204723	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11204726	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11204733	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11204739	0.80[EUR][1000 genomes]
rs1136808	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs11552229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11581757	0.80[EUR][1000 genomes]
rs11582281	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11586422	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs11587444	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs11589458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11803569	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs11803940	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs11804276	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs11807409	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs11807450	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12063547	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs12068264	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12072339	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs12085336	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12086472	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs12089989	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12090215	0.80[EUR][1000 genomes]
rs12096831	0.81[EUR][1000 genomes]
rs12097963	0.80[EUR][1000 genomes]
rs12402939	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12403255	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs12404949	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12409208	0.81[EUR][1000 genomes]
rs12410394	0.81[EUR][1000 genomes]
rs1336899	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs1336900	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1415148	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs1532770	0.86[AFR][1000 genomes]
rs16827671	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17658705	0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap]
rs17660092	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1889740	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2055975	0.83[YRI][hapmap]
rs2089082	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2184833	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs2228099	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2230061	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2256355	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2275235	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2275236	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs2280078	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2864869	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2864873	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2867301	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs2867302	0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap]
rs3754212	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3768005	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs3768013	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3768015	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3768016	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3768018	0.87[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4319334	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4509581	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4537557	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4970982	0.81[EUR][1000 genomes]
rs57818453	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59337856	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6587516	0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap]
rs6587518	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs6657388	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6660084	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6660845	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6661415	0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap]
rs6671737	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6678013	0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap]
rs6693120	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6700022	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs72704639	0.81[EUR][1000 genomes]
rs72704652	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72704654	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72704656	0.83[AFR][1000 genomes]
rs72704658	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7412396	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs7418501	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs7511673	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs7514004	0.81[ASN][1000 genomes]
rs7521592	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7521898	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs7524620	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap]
rs7526489	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7529194	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap]
rs7532045	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7538493	0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap]
rs7540874	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs7556661	0.80[EUR][1000 genomes]
rs868751	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs951281	0.91[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv437169	chr1:150738197-150816886	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv2788	chr1:150755334-150800785	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv160180	chr1:150765276-150772670	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs2864871	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs2864871	RP11-316M1.12	cis	Artery Tibial	GTEx
rs2864871	CTSS	cis	Artery Tibial	GTEx
rs2864871	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs2864871	HORMAD1	cis	Nerve Tibial	GTEx
rs2864871	RP11-316M1.12	cis	lung	GTEx
rs2864871	RP11-316M1.12	cis	Thyroid	GTEx
rs2864871	HORMAD1	cis	Esophagus Mucosa	GTEx
rs2864871	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs2864871	CTSS	cis	multi-tissue	Pritchard
rs2864871	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs2864871	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs2864871	RP11-316M1.12	cis	Whole Blood	GTEx
rs2864871	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs2864871	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs2864871	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs2864871	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs2864871	RP11-316M1.12	cis	Artery Aorta	GTEx
rs2864871	CTSS	cis	Thyroid	GTEx
rs2864871	GOLPH3L	cis	Nerve Tibial	GTEx
rs2864871	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs2864871	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs2864871	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs2864871	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs2864871	RP11-316M1.12	cis	Muscle Skeletal	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150744600-150768200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:150750600-150767600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:150756400-150767600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:150758800-150768400	Weak transcription	Brain Germinal Matrix	brain
5	chr1:150760400-150768200	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:150760400-150771000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:150760600-150768200	Weak transcription	Adipose Nuclei	Adipose
8	chr1:150760600-150768200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:150760600-150768400	Weak transcription	Fetal Lung	lung
10	chr1:150760600-150768800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:150760600-150768800	Weak transcription	Fetal Intestine Small	intestine
12	chr1:150760600-150769000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:150760600-150770200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:150760600-150771000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:150760600-150771400	Weak transcription	Fetal Kidney	kidney
16	chr1:150760600-150779600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:150760800-150768200	Weak transcription	NHLF	lung
18	chr1:150760800-150768600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:150760800-150768800	Weak transcription	Brain Anterior Caudate	brain
20	chr1:150760800-150771000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:150761000-150768000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:150761000-150768000	Weak transcription	Left Ventricle	heart
23	chr1:150761000-150768400	Weak transcription	Colonic Mucosa	Colon
24	chr1:150761200-150768000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:150761200-150768000	Weak transcription	Aorta	Aorta
26	chr1:150761200-150771000	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:150761200-150783200	Weak transcription	GM12878-XiMat	blood
28	chr1:150761800-150770800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:150762000-150767800	Weak transcription	NHDF-Ad	bronchial
30	chr1:150762200-150768800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:150762400-150767800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:150762400-150768000	Weak transcription	Pancreas	Pancrea
33	chr1:150762400-150768800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:150762400-150769000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:150762400-150770200	Weak transcription	Esophagus	oesophagus
36	chr1:150762400-150779200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:150762400-150780000	Weak transcription	NHEK	skin
38	chr1:150762600-150768000	Weak transcription	Placenta	Placenta
39	chr1:150762600-150768200	Weak transcription	Ovary	ovary
40	chr1:150762600-150768600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:150762600-150768800	Weak transcription	Spleen	Spleen
42	chr1:150762800-150768000	Weak transcription	Lung	lung
43	chr1:150763200-150767400	Weak transcription	Fetal Stomach	stomach
44	chr1:150763400-150769600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:150764200-150770600	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr1:150764400-150767800	Weak transcription	Osteobl	bone
47	chr1:150764600-150768000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:150764600-150781600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:150765000-150767600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr1:150765000-150769000	Weak transcription	Primary B cells from cord blood	blood

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