Variant report

Variant	rs3112201
Chromosome Location	chr2:39006603-39006604
allele	G/T
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	chr2:38975156..38979928-chr2:39002986..39007194,11	MCF-7	breast:
3	chr2:38975148..38982473-chr2:39000165..39007764,21	K562	blood:
4	chr2:38976218..38980921-chr2:39003670..39007764,15	K562	blood:
5	chr2:38966114..38968421-chr2:39005419..39007550,2	MCF-7	breast:
6	chr2:39004566..39006965-chr2:39038166..39040437,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223922	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs3099963	1.00[AMR][1000 genomes]
rs3099967	0.82[AFR][1000 genomes]
rs3112202	0.85[AMR][1000 genomes]
rs3112203	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3112206	0.87[AMR][1000 genomes]
rs3112208	0.85[AMR][1000 genomes]
rs7582103	0.94[AFR][1000 genomes];1.00[AMR][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	chr2:39006000-39007400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:39006000-39007400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:39006000-39007600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:39006000-39007600	Weak transcription	Left Ventricle	heart
7	chr2:39006000-39008200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:39006000-39008400	Weak transcription	Placenta	Placenta
9	chr2:39006000-39008600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:39006000-39011800	Weak transcription	Pancreas	Pancrea
11	chr2:39006000-39012400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:39006000-39016000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:39006000-39037600	Weak transcription	Aorta	Aorta
14	chr2:39006000-39037600	Weak transcription	Gastric	stomach
15	chr2:39006200-39006800	Enhancers	Fetal Brain Male	brain
16	chr2:39006200-39007000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr2:39006200-39007600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:39006200-39007800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:39006200-39007800	Weak transcription	Ovary	ovary
20	chr2:39006200-39007800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:39006200-39008600	Weak transcription	Brain Angular Gyrus	brain
22	chr2:39006200-39008600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:39006200-39008600	Weak transcription	HSMM	muscle
24	chr2:39006200-39008600	Weak transcription	NHDF-Ad	bronchial
25	chr2:39006200-39010600	Weak transcription	Stomach Mucosa	stomach
26	chr2:39006200-39025200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:39006200-39029200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:39006200-39029800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:39006200-39031800	Weak transcription	Right Ventricle	heart
30	chr2:39006400-39006800	Enhancers	Primary hematopoietic stem cells	blood
31	chr2:39006400-39007400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:39006400-39007600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:39006400-39007600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:39006400-39007600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr2:39006400-39008200	Weak transcription	Adipose Nuclei	Adipose
36	chr2:39006400-39008200	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:39006400-39008200	Weak transcription	HMEC	breast
38	chr2:39006400-39008200	Weak transcription	K562	blood
39	chr2:39006400-39008200	Weak transcription	NHEK	skin
40	chr2:39006400-39008400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:39006400-39008400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:39006400-39008400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:39006400-39008400	Weak transcription	Brain Anterior Caudate	brain
44	chr2:39006400-39008400	Weak transcription	Brain Substantia Nigra	brain
45	chr2:39006400-39008400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:39006400-39008400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr2:39006400-39008400	Weak transcription	HSMMtube	muscle
48	chr2:39006400-39008400	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr2:39006400-39008400	Weak transcription	NHLF	lung
50	chr2:39006400-39008600	Weak transcription	H1 Cell Line	embryonic stem cell

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