Variant report

Variant	rs28369929
Chromosome Location	chr2:100105476-100105477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:99950963..99955972-chr2:100104881..100108306,7	MCF-7	breast:
2	chr2:99485026..99487433-chr2:100105196..100107704,3	MCF-7	breast:
3	chr2:100075556..100080404-chr2:100103648..100108163,7	K562	blood:
4	chr2:100064922..100067755-chr2:100103657..100105818,3	MCF-7	breast:
5	chr2:99950324..99955285-chr2:100104603..100108030,8	MCF-7	breast:
6	chr2:99951055..99957153-chr2:100104418..100108530,14	K562	blood:
7	chr2:100104533..100107300-chr2:100936927..100940750,3	MCF-7	breast:
8	chr2:99796217..99798600-chr2:100104908..100107681,3	K562	blood:
9	chr2:100104879..100106389-chr2:100120710..100122893,2	MCF-7	breast:
10	chr2:99796217..99799127-chr2:100105224..100108883,4	K562	blood:
11	chr2:99951256..99955616-chr2:100104663..100107649,9	K562	blood:
12	chr2:100019850..100022413-chr2:100104870..100107869,3	MCF-7	breast:
13	chr2:100091970..100094649-chr2:100104238..100106048,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000185414	Chromatin interaction
ENSG00000158411	Chromatin interaction
ENSG00000135945	Chromatin interaction
ENSG00000170500	Chromatin interaction
ENSG00000115514	Chromatin interaction
ENSG00000158417	Chromatin interaction
ENSG00000273306	Chromatin interaction
ENSG00000241962	Chromatin interaction
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10173883	0.85[EUR][1000 genomes]
rs10175852	0.81[EUR][1000 genomes]
rs10176205	0.85[EUR][1000 genomes]
rs10179435	0.83[EUR][1000 genomes]
rs10179697	0.85[EUR][1000 genomes]
rs10180138	0.83[EUR][1000 genomes]
rs10180688	0.81[EUR][1000 genomes]
rs10186223	0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs10207435	0.83[EUR][1000 genomes]
rs10210257	0.83[EUR][1000 genomes]
rs10210346	0.83[EUR][1000 genomes]
rs10469848	0.82[EUR][1000 genomes]
rs10496337	0.83[EUR][1000 genomes]
rs12992356	0.82[CEU][hapmap]
rs13401163	0.81[EUR][1000 genomes]
rs13405400	0.85[EUR][1000 genomes]
rs13409359	0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs13415713	0.85[EUR][1000 genomes]
rs13416265	0.81[EUR][1000 genomes]
rs13419448	0.83[EUR][1000 genomes]
rs13420087	0.85[EUR][1000 genomes]
rs13426758	0.81[EUR][1000 genomes]
rs13427424	0.81[EUR][1000 genomes]
rs13429185	0.81[EUR][1000 genomes]
rs13429806	0.83[EUR][1000 genomes]
rs13430962	0.82[MEX][hapmap];0.85[EUR][1000 genomes]
rs13432046	0.83[EUR][1000 genomes]
rs1922625	0.82[MEX][hapmap]
rs1922626	0.87[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs28369949	0.81[EUR][1000 genomes]
rs28382945	0.81[EUR][1000 genomes]
rs28382947	0.81[EUR][1000 genomes]
rs28745279	0.81[EUR][1000 genomes]
rs3087399	0.83[EUR][1000 genomes]
rs3828162	0.82[MEX][hapmap]
rs4522654	0.82[MEX][hapmap]
rs4851202	0.81[EUR][1000 genomes]
rs7579143	0.82[MEX][hapmap]
rs7582085	0.83[EUR][1000 genomes]
rs7582133	0.83[EUR][1000 genomes]
rs7585532	0.83[EUR][1000 genomes]
rs9308819	0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs9308821	0.83[EUR][1000 genomes]
rs9308822	0.85[EUR][1000 genomes]
rs9308823	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv535841	chr2:100072790-100112121	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv1806302	chr2:100094799-100123030	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3457028	chr2:100101720-100107018	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
6	esv3487602	chr2:100102570-100106918	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
7	esv3457027	chr2:100103045-100105893	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	esv3457029	chr2:100103118-100105501	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	nsv821279	chr2:100103534-100105532	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	nsv829580	chr2:100103534-100105532	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	esv1843390	chr2:100103740-100106224	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
12	esv1809009	chr2:100103752-100109251	Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv582524	chr2:100103752-100110353	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	esv3354592	chr2:100104020-100108718	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	esv3446078	chr2:100104120-100107168	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28369929	LIPT1	cis	cerebellum	SCAN
rs28369929	TSGA10	cis	cerebellum	SCAN
rs28369929	LYG1	cis	parietal	SCAN
rs28369929	ARID5A	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100103600-100107400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr2:100103800-100107000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:100104400-100107000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:100104600-100105800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:100104600-100107000	Active TSS	GM12878-XiMat	blood
6	chr2:100104600-100107200	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr2:100104600-100107400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr2:100104600-100107400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:100104800-100105600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:100104800-100105600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:100104800-100105600	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr2:100104800-100105600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr2:100104800-100105800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr2:100104800-100106200	Active TSS	Right Atrium	heart
15	chr2:100104800-100107000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:100104800-100107000	Active TSS	Fetal Thymus	thymus
17	chr2:100104800-100107000	Active TSS	HMEC	breast
18	chr2:100104800-100107000	Active TSS	NHEK	skin
19	chr2:100104800-100107400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:100104800-100107400	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr2:100104800-100107400	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr2:100104800-100107600	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr2:100105000-100105600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:100105000-100105600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:100105000-100105600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr2:100105000-100105600	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr2:100105000-100105600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr2:100105000-100105600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr2:100105000-100105600	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr2:100105000-100105600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr2:100105000-100105600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:100105000-100105600	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr2:100105000-100105600	Flanking Active TSS	Rectal Smooth Muscle	rectum
34	chr2:100105000-100105600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr2:100105000-100105800	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr2:100105000-100105800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr2:100105000-100105800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr2:100105000-100105800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:100105000-100105800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr2:100105000-100105800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr2:100105000-100106000	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr2:100105000-100106000	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr2:100105000-100106000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:100105000-100107000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr2:100105000-100107000	Active TSS	Fetal Intestine Small	intestine
46	chr2:100105000-100107000	Active TSS	Stomach Smooth Muscle	stomach
47	chr2:100105000-100107000	Active TSS	NH-A	brain
48	chr2:100105000-100107200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:100105000-100107200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:100105000-100107200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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