Variant report

Variant	rs1188816
Chromosome Location	chr6:88055831-88055832
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	chr6:88030970..88032536-chr6:88054131..88056313,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226524	Chromatin interaction
ENSG00000111850	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1145712	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1145713	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1145714	0.81[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1145715	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1145716	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11759727	0.85[ASN][1000 genomes]
rs1188806	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1188817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1188818	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1188819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203162	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1203163	0.89[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1203164	0.85[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12194354	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12211627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201289	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1630494	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1739886	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1746444	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1753152	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1753159	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs181491	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2207144	0.83[CHB][hapmap]
rs2236048	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2257153	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs242263	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs242264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs242265	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs242266	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs242268	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs242269	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs242274	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs242275	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs242276	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs242277	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs242282	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2983136	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs368267	0.81[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs374792	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs377288	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs379455	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs381741	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs381798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs382956	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs383692	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs384318	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs385210	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3857486	0.81[AMR][1000 genomes]
rs392807	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs397516	0.81[CHB][hapmap];0.91[ASN][1000 genomes]
rs398140	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs406981	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs410683	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs411606	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs413687	0.81[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs414453	0.81[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs440296	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs452315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4707345	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4707355	0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs490447	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs540975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs541170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6908834	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6913159	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6921673	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6926686	0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6932641	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6938885	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6939075	0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6940325	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7752414	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs827433	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs910564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs910565	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9294376	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9444488	0.81[AMR][1000 genomes]
rs9444490	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9444491	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9450630	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9450636	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs9450638	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs9450646	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9450651	0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9450653	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9450701	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking 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	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1188816	C6orf164	cis	Nerve Tibial	GTEx
rs1188816	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs1188816	C6orf162	cis	multi-tissue	Pritchard
rs1188816	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs1188816	Hs.485895	cis	multi-tissue	Pritchard
rs1188816	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs1188816	ZNF292	cis	Lymphoblastoid	GTEx
rs1188816	C6orf164	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88033200-88056400	Weak transcription	Liver	Liver
2	chr6:88033200-88062200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr6:88039000-88068400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:88039000-88078400	Weak transcription	Fetal Stomach	stomach
5	chr6:88039400-88061200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:88040200-88075800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:88040600-88116800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:88043600-88058400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:88043800-88056400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:88043800-88056800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr6:88043800-88061400	Weak transcription	Gastric	stomach
12	chr6:88043800-88068400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:88044000-88056000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr6:88044000-88071400	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:88044400-88056000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:88044400-88056800	Weak transcription	Fetal Thymus	thymus
17	chr6:88044400-88076000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:88044800-88072600	Weak transcription	Adipose Nuclei	Adipose
19	chr6:88044800-88075600	Weak transcription	Fetal Lung	lung
20	chr6:88045000-88059800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:88047200-88056600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:88048200-88059000	Weak transcription	Fetal Brain Female	brain
23	chr6:88049200-88066800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:88049600-88061000	Weak transcription	Left Ventricle	heart
25	chr6:88050200-88062000	Weak transcription	Fetal Heart	heart
26	chr6:88050800-88060400	Weak transcription	Osteobl	bone
27	chr6:88051200-88071200	Weak transcription	Ovary	ovary
28	chr6:88051600-88070000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:88052600-88056800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:88053600-88056000	Weak transcription	Brain Angular Gyrus	brain
31	chr6:88054000-88056400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:88054200-88059000	Weak transcription	Psoas Muscle	Psoas
33	chr6:88054600-88067400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:88054600-88068400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr6:88054800-88075600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:88054800-88110200	Weak transcription	Primary T cells from cord blood	blood
37	chr6:88055000-88063600	Weak transcription	HSMM	muscle
38	chr6:88055000-88075800	Weak transcription	Primary B cells from cord blood	blood
39	chr6:88055200-88056800	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:88055200-88072800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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