Variant report

Variant	rs2589094
Chromosome Location	chr2:55483020-55483021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55481770..55484795-chr2:55484832..55488632,4	K562	blood:
2	chr2:55480502..55483270-chr2:55485037..55488051,3	K562	blood:
3	chr2:55481797..55485521-chr2:55489463..55492846,3	K562	blood:
4	chr2:55458420..55460562-chr2:55481965..55484831,2	K562	blood:
5	chr2:55476447..55478832-chr2:55481889..55483888,2	K562	blood:
6	chr2:55480148..55483393-chr2:55492366..55494655,3	K562	blood:
7	chr2:55468640..55470171-chr2:55482025..55483624,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085760	Chromatin interaction
ENSG00000162994	Chromatin interaction
ENSG00000143947	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10200120	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1056445	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11357	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12052613	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2576711	0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs2576712	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2576719	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2589080	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2589092	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2589093	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2589096	0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs2589100	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2864826	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2917779	0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2920967	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34348115	0.90[CHB][hapmap];0.89[CHD][hapmap];0.82[MEX][hapmap];0.86[YRI][hapmap]
rs4435493	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs55997390	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56384563	0.83[ASN][1000 genomes]
rs62135146	0.81[ASN][1000 genomes]
rs6545480	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[ASN][1000 genomes]
rs6737227	1.00[JPT][hapmap];0.95[YRI][hapmap]
rs72799507	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7597293	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs934709	0.85[CHB][hapmap];0.89[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3502708	chr2:55481350-55506212	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3502709	chr2:55481350-55506212	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	esv2361297	chr2:55483019-55483022	Strong transcription Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv525025	chr2:55483020-55505456	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2589094	C2orf63	cis	lymphoblastoid	seeQTL
rs2589094	CLHC1	cis	Adipose Subcutaneous	GTEx
rs2589094	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs2589094	CLHC1	cis	Artery Tibial	GTEx
rs2589094	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55461600-55495400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:55461600-55495400	Weak transcription	Stomach Mucosa	stomach
3	chr2:55461800-55493400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:55461800-55495000	Weak transcription	Fetal Brain Male	brain
5	chr2:55462000-55493200	Strong transcription	Duodenum Mucosa	Duodenum
6	chr2:55462200-55490200	Weak transcription	Small Intestine	intestine
7	chr2:55462600-55485800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:55463000-55495400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:55463400-55488200	Weak transcription	Pancreas	Pancrea
10	chr2:55463600-55483800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:55463800-55486200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:55463800-55490400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:55463800-55494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:55463800-55495600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:55464600-55495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:55465400-55490600	Weak transcription	Brain Germinal Matrix	brain
17	chr2:55465600-55486000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:55465600-55494400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:55466000-55493200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr2:55468200-55493400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr2:55468400-55493200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:55468400-55494400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:55468600-55494400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:55468800-55493600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:55468800-55494400	Strong transcription	Adipose Nuclei	Adipose
26	chr2:55468800-55494400	Strong transcription	Liver	Liver
27	chr2:55469400-55492600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr2:55470800-55494200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:55472000-55485000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:55472000-55495200	Weak transcription	Psoas Muscle	Psoas
31	chr2:55473600-55484600	Weak transcription	Hela-S3	cervix
32	chr2:55473600-55490200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:55475000-55485200	Weak transcription	HSMMtube	muscle
34	chr2:55475200-55484800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:55475400-55490000	Weak transcription	Gastric	stomach
36	chr2:55476000-55495400	Weak transcription	HUVEC	blood vessel
37	chr2:55476600-55490000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:55476600-55495400	Weak transcription	Aorta	Aorta
39	chr2:55476600-55495400	Weak transcription	Fetal Heart	heart
40	chr2:55476600-55495600	Weak transcription	Esophagus	oesophagus
41	chr2:55476800-55484800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:55476800-55490200	Weak transcription	Spleen	Spleen
43	chr2:55476800-55495400	Weak transcription	Fetal Kidney	kidney
44	chr2:55477000-55490200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:55477200-55483800	Weak transcription	Lung	lung
46	chr2:55478400-55485000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:55478400-55493400	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:55478400-55494800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:55478600-55483400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:55478800-55483600	Strong transcription	Dnd41	blood

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