Variant report

Variant	rs2603361
Chromosome Location	chr2:33492009-33492010
allele	C/T
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:
7	chr2:33489408..33492344-chr2:33493804..33495896,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188825	Chromatin interaction
ENSG00000049323	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10169788	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10175557	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10175619	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs11124313	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11673950	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11684829	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13391131	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13392154	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13394195	0.86[CEU][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13403065	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs17582516	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3769540	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3769542	0.85[YRI][hapmap]
rs3769544	0.86[EUR][1000 genomes]
rs3769545	0.83[CHB][hapmap]
rs4233909	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4670387	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4670408	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62148881	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62148882	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6543704	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6543705	0.85[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6711027	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6739030	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6739506	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6739725	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6751758	0.86[JPT][hapmap]
rs711234	1.00[CHB][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs711235	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs723043	0.81[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs749454	0.91[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs7565095	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7586227	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7590205	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7605474	0.87[EUR][1000 genomes]
rs817529	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs817532	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs817534	0.89[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs817536	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs817537	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs817539	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9308934	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs971793	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[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:67 , 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	chr2:33487200-33492200	Weak transcription	Right Atrium	heart
8	chr2:33487800-33502400	Weak transcription	Brain Anterior Caudate	brain
9	chr2:33488200-33492400	Strong transcription	Liver	Liver
10	chr2:33489800-33492600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
11	chr2:33489800-33493000	Strong transcription	Aorta	Aorta
12	chr2:33490000-33492400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
13	chr2:33490000-33493000	Enhancers	HMEC	breast
14	chr2:33490000-33499400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:33490200-33493800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:33490600-33492400	Strong transcription	Stomach Smooth Muscle	stomach
17	chr2:33490600-33492600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:33490600-33515600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:33491000-33492200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:33491000-33492400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
21	chr2:33491000-33492400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:33491000-33492400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:33491000-33492400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
24	chr2:33491000-33492400	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr2:33491000-33492400	ZNF genes & repeats	Fetal Muscle Leg	muscle
26	chr2:33491000-33492400	ZNF genes & repeats	Fetal Stomach	stomach
27	chr2:33491000-33492400	ZNF genes & repeats	Gastric	stomach
28	chr2:33491000-33492400	ZNF genes & repeats	Lung	lung
29	chr2:33491000-33492400	ZNF genes & repeats	Spleen	Spleen
30	chr2:33491000-33492400	ZNF genes & repeats	Dnd41	blood
31	chr2:33491000-33492400	ZNF genes & repeats	NH-A	brain
32	chr2:33491000-33492600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:33491000-33492600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:33491000-33492600	ZNF genes & repeats	Ovary	ovary
35	chr2:33491000-33492600	ZNF genes & repeats	NHLF	lung
36	chr2:33491200-33492200	ZNF genes & repeats	Brain Hippocampus Middle	brain
37	chr2:33491200-33492200	ZNF genes & repeats	Brain Substantia Nigra	brain
38	chr2:33491200-33492200	ZNF genes & repeats	Placenta	Placenta
39	chr2:33491200-33492400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:33491200-33492400	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:33491200-33492400	ZNF genes & repeats	Esophagus	oesophagus
42	chr2:33491200-33492400	ZNF genes & repeats	Pancreas	Pancrea
43	chr2:33491200-33492600	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr2:33491200-33492600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:33491200-33492600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
46	chr2:33491200-33493000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:33491200-33495800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:33491400-33492200	Strong transcription	Right Ventricle	heart
49	chr2:33491400-33492600	Weak transcription	HUVEC	blood vessel
50	chr2:33491400-33493600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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