Variant report

Variant	rs1823834
Chromosome Location	chr2:33492739-33492740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:41400425..41402576-chr2:33491310..33492810,2	K562	blood:
2	chr2:33491310..33492830-chr3:73158437..73159956,2	K562	blood:
3	chr17:41392284..41394674-chr2:33491310..33492810,2	K562	blood:
4	chr2:33171933..33174048-chr2:33491328..33494220,2	MCF-7	breast:
5	chr17:41463791..41467360-chr2:33489830..33492830,6	K562	blood:
6	chr2:33491437..33494514-chr2:33496533..33499773,3	K562	blood:

Variant related genes	Relation type
ENSG00000188825	Chromatin interaction
ENSG00000049323	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12987969	0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs1453842	0.85[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap]
rs1463312	0.80[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1463313	1.00[ASW][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2123770	0.81[CHB][hapmap];0.81[CHD][hapmap];0.84[LWK][hapmap];0.88[YRI][hapmap]
rs3769541	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7572682	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs817530	1.00[ASW][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs817531	0.86[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs817533	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	nsv873791	chr2:33489975-33586776	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33466400-33497400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:33466600-33500800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:33472000-33516600	Weak transcription	Psoas Muscle	Psoas
4	chr2:33472600-33492800	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:33486600-33493400	Weak transcription	Fetal Kidney	kidney
6	chr2:33487000-33509800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:33487800-33502400	Weak transcription	Brain Anterior Caudate	brain
8	chr2:33489800-33493000	Strong transcription	Aorta	Aorta
9	chr2:33490000-33493000	Enhancers	HMEC	breast
10	chr2:33490000-33499400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:33490200-33493800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:33490600-33515600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:33491200-33493000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:33491200-33495800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:33491400-33493600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:33491800-33502000	Weak transcription	Brain Angular Gyrus	brain
17	chr2:33491800-33504400	Weak transcription	Colonic Mucosa	Colon
18	chr2:33492000-33493400	Enhancers	Fetal Brain Male	brain
19	chr2:33492000-33493600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:33492000-33494000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:33492000-33495800	Weak transcription	A549	lung
22	chr2:33492000-33515800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:33492200-33493000	Enhancers	NHDF-Ad	bronchial
24	chr2:33492200-33501000	Weak transcription	Placenta	Placenta
25	chr2:33492200-33516600	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:33492200-33516600	Weak transcription	Brain Substantia Nigra	brain
27	chr2:33492400-33492800	Weak transcription	Fetal Lung	lung
28	chr2:33492400-33492800	Weak transcription	Right Atrium	heart
29	chr2:33492400-33493200	Weak transcription	Gastric	stomach
30	chr2:33492400-33493600	Strong transcription	NH-A	brain
31	chr2:33492400-33493800	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:33492400-33494200	Enhancers	Fetal Heart	heart
33	chr2:33492400-33497200	Weak transcription	Right Ventricle	heart
34	chr2:33492400-33499400	Weak transcription	Liver	Liver
35	chr2:33492400-33499600	Weak transcription	Left Ventricle	heart
36	chr2:33492400-33500000	Weak transcription	Fetal Stomach	stomach
37	chr2:33492400-33500800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:33492400-33500800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:33492400-33500800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:33492400-33500800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:33492400-33500800	Weak transcription	Esophagus	oesophagus
42	chr2:33492400-33500800	Weak transcription	Pancreas	Pancrea
43	chr2:33492400-33501000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:33492400-33501800	Weak transcription	Lung	lung
45	chr2:33492400-33502000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:33492400-33502000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr2:33492400-33502000	Weak transcription	Spleen	Spleen
48	chr2:33492400-33547400	Weak transcription	Fetal Intestine Small	intestine
49	chr2:33492600-33492800	Enhancers	Fetal Brain Female	brain
50	chr2:33492600-33493400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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