Variant report

Variant	rs3856409
Chromosome Location	chr2:182644308-182644309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:182642988..182645048-chr2:182649419..182652084,2	MCF-7	breast:
2	chr2:182637643..182640339-chr2:182643105..182646087,2	K562	blood:
3	chr2:182633948..182636625-chr2:182642874..182645576,3	MCF-7	breast:
4	chr2:182640852..182647278-chr2:182753659..182759466,8	MCF-7	breast:
5	chr2:182607754..182610129-chr2:182643421..182645171,2	MCF-7	breast:
6	chr2:182642708..182644786-chr2:182755932..182758313,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260742	Chromatin interaction
ENSG00000138434	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17365505	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs8192556	1.00[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

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182636400-182645800	Weak transcription	Pancreas	Pancrea
2	chr2:182640000-182644400	Weak transcription	HSMM	muscle
3	chr2:182640000-182644400	Weak transcription	HSMMtube	muscle
4	chr2:182640000-182645000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr2:182640200-182644800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:182640600-182646400	Enhancers	HUVEC	blood vessel
7	chr2:182640800-182644400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:182641800-182649600	Enhancers	Fetal Intestine Large	intestine
9	chr2:182641800-182650000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:182642200-182646200	Enhancers	NHEK	skin
11	chr2:182642200-182657200	Enhancers	Hela-S3	cervix
12	chr2:182642400-182644600	Enhancers	Stomach Mucosa	stomach
13	chr2:182642400-182645200	Enhancers	Fetal Kidney	kidney
14	chr2:182642400-182645400	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr2:182642400-182646000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:182642400-182646600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:182642400-182647200	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr2:182642400-182647600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:182642600-182646200	Enhancers	HMEC	breast
20	chr2:182643000-182645400	Enhancers	Osteobl	bone
21	chr2:182643200-182645000	Enhancers	A549	lung
22	chr2:182643200-182645400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:182643200-182645600	Enhancers	Brain Anterior Caudate	brain
24	chr2:182643200-182645600	Enhancers	NHLF	lung
25	chr2:182643200-182645800	Enhancers	Brain Hippocampus Middle	brain
26	chr2:182643200-182645800	Enhancers	NH-A	brain
27	chr2:182643200-182646000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:182643200-182646200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:182643200-182646400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:182643400-182644800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:182643400-182645200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr2:182643400-182645200	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr2:182643400-182645400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:182643400-182645600	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr2:182643400-182645600	Enhancers	Brain Substantia Nigra	brain
36	chr2:182643400-182645600	Enhancers	Placenta	Placenta
37	chr2:182643400-182646000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:182643400-182646000	Enhancers	Muscle Satellite Cultured Cells	--
39	chr2:182643400-182646200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:182643400-182646200	Enhancers	Fetal Muscle Leg	muscle
41	chr2:182643400-182646400	Enhancers	Small Intestine	intestine
42	chr2:182643400-182646600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:182643400-182646600	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr2:182643400-182646800	Enhancers	HepG2	liver
45	chr2:182643400-182647000	Enhancers	Fetal Intestine Small	intestine
46	chr2:182643600-182644400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:182643600-182645000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:182643600-182645400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr2:182643800-182644400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:182643800-182644800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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