Variant report

Variant	rs13391733
Chromosome Location	chr2:182648425-182648426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:182647541..182657734-chr2:182753295..182760748,23	MCF-7	breast:
2	chr2:182646086..182659083-chr2:182754079..182762654,36	MCF-7	breast:
3	chr2:182642047..182644183-chr2:182648360..182651289,2	K562	blood:

Variant related genes	Relation type
ENSG00000138434	Chromatin interaction
ENSG00000260742	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10166975	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10171629	0.85[AFR][1000 genomes]
rs10176757	0.82[YRI][hapmap]
rs10189187	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10191082	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10201303	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10203440	0.85[AFR][1000 genomes]
rs13384259	0.80[AFR][1000 genomes]
rs13396152	0.89[AFR][1000 genomes]
rs13401364	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13404156	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1528024	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1528025	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1528026	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1528027	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16867498	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2368235	0.84[EUR][1000 genomes]
rs4597477	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6707164	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6707654	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6720109	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6723011	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6736341	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6736766	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6739707	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6741761	0.80[AFR][1000 genomes]
rs6751464	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6754819	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73032623	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7600976	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1001558	chr2:182590009-182732738	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13391733	LOC647288///LOC730587	trans	lymphoblastoid	RTeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182641800-182649600	Enhancers	Fetal Intestine Large	intestine
2	chr2:182641800-182650000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:182642200-182657200	Enhancers	Hela-S3	cervix
4	chr2:182645200-182651800	Weak transcription	Thymus	Thymus
5	chr2:182645400-182648600	Weak transcription	Osteobl	bone
6	chr2:182645400-182649200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:182645400-182649200	Weak transcription	HSMMtube	muscle
8	chr2:182645400-182649200	Weak transcription	NHDF-Ad	bronchial
9	chr2:182645400-182650600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:182645600-182649000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:182645800-182648600	Weak transcription	NH-A	brain
12	chr2:182645800-182649000	Weak transcription	HSMM	muscle
13	chr2:182646000-182648800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:182646000-182649200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:182646000-182651200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:182646000-182651800	Weak transcription	Fetal Thymus	thymus
17	chr2:182646200-182648600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:182646200-182648600	Weak transcription	HMEC	breast
19	chr2:182646200-182648600	Weak transcription	NHEK	skin
20	chr2:182646200-182649200	Weak transcription	Fetal Lung	lung
21	chr2:182646200-182651000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:182646200-182651200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr2:182646200-182651200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:182646400-182649200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:182646400-182649200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:182646400-182650200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:182646400-182651600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:182646400-182651600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr2:182646600-182648600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:182646600-182648600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:182646600-182651200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:182646600-182651200	Weak transcription	Pancreas	Pancrea
33	chr2:182646600-182653400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:182646600-182654800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:182646800-182648800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:182647200-182652600	Enhancers	HepG2	liver
37	chr2:182647200-182652800	Enhancers	Stomach Mucosa	stomach
38	chr2:182647400-182649200	Enhancers	NHLF	lung
39	chr2:182647400-182653000	Enhancers	Fetal Intestine Small	intestine
40	chr2:182647600-182650600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:182647800-182648800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:182647800-182649200	Weak transcription	HUVEC	blood vessel
43	chr2:182647800-182650000	Enhancers	Fetal Kidney	kidney
44	chr2:182647800-182650200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:182648000-182648800	Enhancers	Gastric	stomach
46	chr2:182648000-182649200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:182648000-182649200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr2:182648000-182649400	Enhancers	A549	lung
49	chr2:182648000-182657200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:182648200-182648800	Enhancers	Small Intestine	intestine

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