Variant report

Variant	rs11808099
Chromosome Location	chr1:171688790-171688791
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171686305..171689252-chr1:171710111..171712104,2	K562	blood:
2	chr1:171688591..171690829-chr1:171750359..171752886,2	MCF-7	breast:
3	chr1:171687308..171689359-chr1:171700947..171702726,2	K562	blood:

Variant related genes	Relation type
ENSG00000010165	Chromatin interaction
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1001373	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489249	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10489251	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1052676	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10903	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913489	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10913490	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10913492	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10913511	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913514	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913529	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913565	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913582	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10913587	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11576221	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11577073	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11577197	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11577745	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11578179	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11578699	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11578723	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11579698	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11580415	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11580522	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11583920	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590680	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11590714	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11799420	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11801846	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11803174	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11811780	0.85[EUR][1000 genomes]
rs12119232	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12123727	0.83[EUR][1000 genomes]
rs12127026	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12128536	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12132221	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15655	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17649050	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17649068	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2298914	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2421911	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3766653	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55670848	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58455759	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6656003	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659874	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6667559	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6669263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6678890	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6679354	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7528057	0.83[EUR][1000 genomes]
rs7536436	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7536543	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9661596	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9662174	0.81[EUR][1000 genomes]
rs9662853	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1800458	chr1:171667663-171701129	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11808099	VAMP4	Cis_1M	lymphoblastoid	RTeQTL
rs11808099	VAMP4	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171665000-171692000	Weak transcription	Brain Substantia Nigra	brain
2	chr1:171665600-171705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:171665600-171708800	Weak transcription	Brain Angular Gyrus	brain
4	chr1:171666000-171705400	Weak transcription	Pancreas	Pancrea
5	chr1:171666800-171692000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:171666800-171692000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:171666800-171692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:171666800-171702400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:171667000-171692000	Weak transcription	Fetal Brain Female	brain
10	chr1:171667000-171692200	Weak transcription	Brain Anterior Caudate	brain
11	chr1:171667600-171692000	Weak transcription	Fetal Lung	lung
12	chr1:171667800-171688800	Weak transcription	Spleen	Spleen
13	chr1:171667800-171692000	Weak transcription	Fetal Thymus	thymus
14	chr1:171668600-171692400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:171668800-171705400	Weak transcription	Right Ventricle	heart
16	chr1:171668800-171708200	Weak transcription	Small Intestine	intestine
17	chr1:171669600-171705400	Weak transcription	Fetal Brain Male	brain
18	chr1:171670600-171692000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:171672800-171692000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:171674000-171696400	Weak transcription	HSMM	muscle
21	chr1:171674600-171692200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:171674800-171696800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:171674800-171697200	Weak transcription	Ovary	ovary
24	chr1:171677000-171692000	Weak transcription	GM12878-XiMat	blood
25	chr1:171677200-171692000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:171677200-171692200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:171677200-171698800	Weak transcription	Aorta	Aorta
28	chr1:171677400-171692200	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:171678000-171692000	Weak transcription	Fetal Intestine Small	intestine
30	chr1:171678800-171692000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:171679000-171692000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:171679000-171693800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:171679000-171696000	Weak transcription	Fetal Intestine Large	intestine
34	chr1:171683200-171692800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr1:171684600-171692000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:171685200-171692000	Weak transcription	Fetal Muscle Leg	muscle
37	chr1:171685200-171692000	Weak transcription	Fetal Stomach	stomach
38	chr1:171685200-171692000	Weak transcription	Lung	lung
39	chr1:171685200-171692200	Weak transcription	Left Ventricle	heart
40	chr1:171685600-171692000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:171686000-171689800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:171686000-171696800	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:171686000-171699000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr1:171686400-171692000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:171686400-171692000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:171686400-171696800	Weak transcription	NH-A	brain
47	chr1:171686600-171692000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:171686600-171692000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:171686600-171692000	Weak transcription	Adipose Nuclei	Adipose
50	chr1:171686600-171692000	Weak transcription	Thymus	Thymus

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