Variant report

Variant	rs10168028
Chromosome Location	chr2:39007797-39007798
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38974982..38979904-chr2:39002191..39014206,31	MCF-7	breast:
2	chr2:38993209..38995928-chr2:39007575..39009225,2	MCF-7	breast:
3	chr2:38977058..38979764-chr2:39007414..39010440,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10200935	1.00[ASN][1000 genomes]
rs10203173	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13390845	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13393938	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13412656	1.00[ASN][1000 genomes]
rs13418902	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13419028	1.00[ASN][1000 genomes]
rs13425948	1.00[ASN][1000 genomes]
rs1541877	1.00[ASN][1000 genomes]
rs17023076	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1897327	1.00[ASN][1000 genomes]
rs3099969	1.00[ASN][1000 genomes]
rs3112187	1.00[ASN][1000 genomes]
rs3112190	1.00[ASN][1000 genomes]
rs6753616	1.00[ASN][1000 genomes]
rs6760965	1.00[ASN][1000 genomes]
rs72797353	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72797362	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers 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	111 gene(s)	inside rSNPs	diseases
4	nsv1014616	chr2:38985472-39022893	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39005800-39007800	Weak transcription	Lung	lung
2	chr2:39005800-39037400	Weak transcription	Esophagus	oesophagus
3	chr2:39006000-39008200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:39006000-39008400	Weak transcription	Placenta	Placenta
5	chr2:39006000-39008600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:39006000-39011800	Weak transcription	Pancreas	Pancrea
7	chr2:39006000-39012400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:39006000-39016000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:39006000-39037600	Weak transcription	Aorta	Aorta
10	chr2:39006000-39037600	Weak transcription	Gastric	stomach
11	chr2:39006200-39007800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:39006200-39007800	Weak transcription	Ovary	ovary
13	chr2:39006200-39007800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:39006200-39008600	Weak transcription	Brain Angular Gyrus	brain
15	chr2:39006200-39008600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:39006200-39008600	Weak transcription	HSMM	muscle
17	chr2:39006200-39008600	Weak transcription	NHDF-Ad	bronchial
18	chr2:39006200-39010600	Weak transcription	Stomach Mucosa	stomach
19	chr2:39006200-39025200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:39006200-39029200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:39006200-39029800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:39006200-39031800	Weak transcription	Right Ventricle	heart
23	chr2:39006400-39008200	Weak transcription	Adipose Nuclei	Adipose
24	chr2:39006400-39008200	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:39006400-39008200	Weak transcription	HMEC	breast
26	chr2:39006400-39008200	Weak transcription	K562	blood
27	chr2:39006400-39008200	Weak transcription	NHEK	skin
28	chr2:39006400-39008400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:39006400-39008400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:39006400-39008400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:39006400-39008400	Weak transcription	Brain Anterior Caudate	brain
32	chr2:39006400-39008400	Weak transcription	Brain Substantia Nigra	brain
33	chr2:39006400-39008400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:39006400-39008400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:39006400-39008400	Weak transcription	HSMMtube	muscle
36	chr2:39006400-39008400	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr2:39006400-39008400	Weak transcription	NHLF	lung
38	chr2:39006400-39008600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:39006400-39008600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:39006400-39008600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:39006400-39008600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr2:39006400-39008600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr2:39006400-39008600	Weak transcription	HUVEC	blood vessel
44	chr2:39006400-39009600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:39006400-39010400	Strong transcription	Fetal Intestine Small	intestine
46	chr2:39006400-39010400	Weak transcription	NH-A	brain
47	chr2:39006400-39011200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr2:39006400-39018800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:39006400-39024000	Weak transcription	Osteobl	bone
50	chr2:39006400-39025200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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