Variant report

Variant	rs2945554
Chromosome Location	chr8:95939594-95939595
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:95938390..95942310-chr8:95942961..95947841,5	MCF-7	breast:
2	chr8:95938299..95940006-chr8:95957617..95959373,2	K562	blood:
3	chr8:95937635..95940047-chr8:95941956..95944117,3	K562	blood:
4	chr8:95937992..95941627-chr8:95953308..95955835,4	MCF-7	breast:
5	chr8:95938382..95942226-chr8:95942291..95944810,3	MCF-7	breast:

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10086284	1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs10098778	1.00[CHB][hapmap]
rs10099941	1.00[CHB][hapmap]
rs10104909	1.00[CHB][hapmap]
rs10112447	0.86[EUR][1000 genomes]
rs1011795	0.84[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1011796	0.84[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1017634	0.88[AFR][1000 genomes]
rs10441538	0.84[CHB][hapmap]
rs10956928	0.93[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs10956929	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs10956930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10956931	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10956932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1129152	0.86[CHB][hapmap]
rs11784717	0.85[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap]
rs11996455	0.86[CHB][hapmap]
rs12541035	0.93[ASN][1000 genomes]
rs12545596	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12548367	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12548999	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12549003	1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs12550765	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs12679044	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs13255935	0.85[CHB][hapmap]
rs13257021	0.85[CHB][hapmap]
rs13271375	0.86[CHB][hapmap]
rs13282419	0.84[AMR][1000 genomes]
rs1453377	1.00[CHB][hapmap]
rs1453379	1.00[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs16893776	1.00[CHB][hapmap]
rs1971212	0.82[AFR][1000 genomes]
rs2013597	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2013995	0.94[AFR][1000 genomes]
rs2123647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2278891	0.84[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs2340583	0.90[ASN][1000 genomes]
rs2459963	0.84[AFR][1000 genomes]
rs2459964	0.90[AFR][1000 genomes]
rs2459965	0.89[ASW][hapmap];0.91[LWK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs2467672	0.84[AFR][1000 genomes]
rs2467674	0.81[AFR][1000 genomes]
rs2467676	0.90[AFR][1000 genomes]
rs2515237	0.87[AFR][1000 genomes]
rs2924477	0.88[ASN][1000 genomes]
rs2945563	0.86[ASN][1000 genomes]
rs2956210	0.85[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap]
rs2956216	0.85[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs3019175	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3019182	0.95[ASN][1000 genomes]
rs34293080	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36118131	0.88[AFR][1000 genomes]
rs3802193	1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs4570121	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4734291	0.87[JPT][hapmap]
rs4734293	0.83[EUR][1000 genomes]
rs4734295	0.81[CHB][hapmap]
rs4735328	0.85[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs4735329	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4735330	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4735331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4735332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4735334	0.85[CHB][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap]
rs4735336	1.00[CHB][hapmap]
rs4735337	1.00[CHB][hapmap]
rs4735339	1.00[CHB][hapmap]
rs477653	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs535322	0.95[ASN][1000 genomes]
rs550418	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs550564	0.88[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs551270	0.85[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs61537129	0.89[ASN][1000 genomes]
rs6471497	0.88[CEU][hapmap]
rs6471499	0.84[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs6471500	0.84[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs6471501	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6471503	1.00[CHB][hapmap]
rs6471504	0.86[CHB][hapmap]
rs683832	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs6982393	1.00[CHB][hapmap]
rs6983000	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6987256	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs6987400	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6991067	0.86[CHB][hapmap]
rs7001535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7004862	0.86[CHB][hapmap]
rs7005317	0.85[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs7015841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7017487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs726816	0.92[CHB][hapmap]
rs7760	0.83[ASW][hapmap];0.80[YRI][hapmap]
rs7820818	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7827478	1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs7845219	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs896849	0.83[ASW][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes]
rs896850	0.83[EUR][1000 genomes]
rs896851	0.92[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs896854	0.85[CHB][hapmap]
rs9643350	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9643351	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9643352	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9643353	0.84[CEU][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv891203	chr8:95883232-95948202	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv891204	chr8:95883232-95965135	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv508520	chr8:95939373-96140068	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2945554	INTS8	cis	cerebellum	SCAN
rs2945554	SLC26A7	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95909400-95941000	Weak transcription	Ovary	ovary
2	chr8:95909400-95941200	Weak transcription	Fetal Stomach	stomach
3	chr8:95909600-95941800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr8:95909800-95940600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr8:95910000-95940200	Weak transcription	Thymus	Thymus
6	chr8:95910800-95940200	Weak transcription	Hela-S3	cervix
7	chr8:95918000-95940200	Weak transcription	Brain Anterior Caudate	brain
8	chr8:95918600-95947400	Weak transcription	Small Intestine	intestine
9	chr8:95919000-95941200	Weak transcription	Left Ventricle	heart
10	chr8:95919200-95948600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr8:95926200-95939600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr8:95926200-95946400	Weak transcription	Stomach Mucosa	stomach
13	chr8:95926400-95941200	Weak transcription	Pancreas	Pancrea
14	chr8:95927000-95940400	Weak transcription	Lung	lung
15	chr8:95928600-95939600	Weak transcription	Fetal Intestine Large	intestine
16	chr8:95928600-95939600	Weak transcription	Dnd41	blood
17	chr8:95928600-95940200	Weak transcription	Fetal Kidney	kidney
18	chr8:95928600-95940200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr8:95928600-95941200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr8:95928600-95941200	Weak transcription	Fetal Intestine Small	intestine
21	chr8:95928800-95939800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr8:95929800-95940600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr8:95930200-95941800	Weak transcription	Spleen	Spleen
24	chr8:95930600-95939800	Weak transcription	Fetal Lung	lung
25	chr8:95930600-95940800	Weak transcription	Aorta	Aorta
26	chr8:95930600-95948600	Weak transcription	Gastric	stomach
27	chr8:95931800-95950000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr8:95932000-95940400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr8:95932400-95940600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr8:95932800-95940200	Weak transcription	HSMMtube	muscle
31	chr8:95933000-95939600	Weak transcription	HSMM	muscle
32	chr8:95933000-95941200	Weak transcription	Esophagus	oesophagus
33	chr8:95933400-95960600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr8:95933600-95940000	Weak transcription	Brain Substantia Nigra	brain
35	chr8:95933600-95940200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr8:95933600-95940800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr8:95933600-95941200	Weak transcription	K562	blood
38	chr8:95933600-95942000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr8:95933600-95949600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr8:95933800-95941400	Weak transcription	Fetal Heart	heart
41	chr8:95934000-95940000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr8:95934000-95940800	Weak transcription	Brain Hippocampus Middle	brain
43	chr8:95934200-95940200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr8:95934200-95940200	Weak transcription	Fetal Brain Female	brain
45	chr8:95934200-95941400	Weak transcription	Right Ventricle	heart
46	chr8:95934400-95940600	Weak transcription	Fetal Brain Male	brain
47	chr8:95935200-95956400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr8:95935400-95939600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr8:95935400-95940200	Weak transcription	NHLF	lung
50	chr8:95935400-95941200	Weak transcription	HepG2	liver

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