Variant report

Variant	rs12634699
Chromosome Location	chr3:150439822-150439823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr3:150438944-150439848	SK-N-SH	brain:	n/a	chr3:150439266-150439285
2	BHLHE40	chr3:150439095-150439845	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150320523..150322678-chr3:150439269..150441009,2	MCF-7	breast:
2	chr3:150320885..150322876-chr3:150438158..150440375,2	K562	blood:
3	chr3:150438851..150440084-chr3:150582767..150583714,6	MCF-7	breast:
4	chr3:150433681..150449199-chr3:150473254..150487048,35	MCF-7	breast:
5	chr3:150439194..150440771-chr3:150583171..150584932,2	MCF-7	breast:
6	chr3:150419945..150423964-chr3:150439302..150443369,4	MCF-7	breast:
7	chr3:150439035..150439884-chr3:150583116..150584203,3	MCF-7	breast:
8	chr3:150439162..150440062-chr3:150496902..150497867,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000244668	TF binding region
ENSG00000181788	Chromatin interaction
ENSG00000163645	Chromatin interaction
ENSG00000244265	Chromatin interaction
ENSG00000198843	Chromatin interaction
ENSG00000240137	Chromatin interaction
ENSG00000120742	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12494272	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12630292	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12638096	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085974	0.81[ASN][1000 genomes]
rs13086267	0.81[ASN][1000 genomes]
rs1897489	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1897491	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28460384	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28790675	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4558804	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55838848	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6766333	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6784407	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6807493	0.81[ASN][1000 genomes]
rs73869279	0.81[ASN][1000 genomes]
rs7641475	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7648424	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7650706	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9682958	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9814796	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9848451	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9858987	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9869495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9876621	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150422200-150443200	Weak transcription	Lung	lung
2	chr3:150422400-150443000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:150422600-150441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:150423200-150451600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:150429200-150444600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:150429200-150457600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:150430000-150455000	Weak transcription	Primary T cells from cord blood	blood
8	chr3:150430400-150441600	Weak transcription	Thymus	Thymus
9	chr3:150430800-150454000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:150439200-150442200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr3:150439400-150440000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr3:150439400-150440000	Enhancers	Hela-S3	cervix
13	chr3:150439400-150440000	Enhancers	NHEK	skin
14	chr3:150439400-150440000	Enhancers	Osteobl	bone
15	chr3:150439400-150440400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:150439400-150441400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:150439400-150446800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:150439600-150440600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:150439600-150440600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:150439600-150443000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:150439600-150444400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:150439600-150444800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:150439800-150440800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:150439800-150441000	Enhancers	K562	blood
25	chr3:150439800-150441200	Weak transcription	Fetal Thymus	thymus
26	chr3:150439800-150441800	Weak transcription	Brain Germinal Matrix	brain
27	chr3:150439800-150441800	Weak transcription	Ovary	ovary
28	chr3:150439800-150441800	Weak transcription	HepG2	liver
29	chr3:150439800-150442000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:150439800-150442600	Weak transcription	Placenta	Placenta
31	chr3:150439800-150443000	Weak transcription	Colonic Mucosa	Colon
32	chr3:150439800-150443000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:150439800-150443000	Weak transcription	Fetal Intestine Large	intestine
34	chr3:150439800-150443000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:150439800-150443200	Weak transcription	Fetal Intestine Small	intestine
36	chr3:150439800-150444600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:150439800-150444800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:150439800-150444800	Weak transcription	Adipose Nuclei	Adipose
39	chr3:150439800-150444800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr3:150439800-150444800	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:150439800-150445600	Weak transcription	Gastric	stomach
42	chr3:150439800-150457600	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:150439800-150459000	Weak transcription	Brain Inferior Temporal Lobe	brain

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