Variant report

Variant	rs2237659
Chromosome Location	chr7:106847492-106847493
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:106841974..106843940-chr7:106847198..106849024,2	MCF-7	breast:
2	chr7:106838224..106841860-chr7:106847097..106850411,5	K562	blood:
3	chr7:106838412..106842841-chr7:106847097..106851611,6	K562	blood:
4	chr7:106844012..106846635-chr7:106846646..106848809,2	K562	blood:
5	chr7:106833261..106834948-chr7:106846398..106848548,2	K562	blood:
6	chr7:106845720..106848557-chr7:107077031..107079776,2	K562	blood:

Variant related genes	Relation type
ENSG00000272072	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12112877	0.83[ASN][1000 genomes]
rs12670688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12672451	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13230144	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17153981	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17154040	0.81[ASN][1000 genomes]
rs2107317	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2237658	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237660	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237661	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237662	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2237665	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2251838	0.81[MKK][hapmap]
rs2283038	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2301801	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2395868	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2395869	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2536501	0.81[MKK][hapmap]
rs34021916	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3801964	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3801966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4730220	0.87[ASN][1000 genomes]
rs62482493	0.83[ASN][1000 genomes]
rs62483619	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62483623	0.85[ASN][1000 genomes]
rs62483627	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62483629	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62483633	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62483634	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62483640	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62483641	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7777950	0.81[ASN][1000 genomes]
rs7785892	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7803151	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831087	chr7:106673465-106872460	Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2237659	GPR22	cis	multi-tissue	Pritchard
rs2237659	COG5	cis	parietal	SCAN
rs2237659	BCAP29	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106815200-106849400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr7:106817400-106851400	Strong transcription	Primary B cells from peripheral blood	blood
3	chr7:106819600-106851800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr7:106819800-106851600	Strong transcription	Dnd41	blood
5	chr7:106820000-106851200	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr7:106820000-106851600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr7:106820200-106848400	Strong transcription	Placenta	Placenta
8	chr7:106820200-106851200	Strong transcription	Primary B cells from cord blood	blood
9	chr7:106820200-106851800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:106820200-106851800	Strong transcription	Fetal Thymus	thymus
11	chr7:106820400-106848200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:106821000-106848400	Strong transcription	Liver	Liver
13	chr7:106821000-106854600	Strong transcription	Primary T cells from cord blood	blood
14	chr7:106821200-106851800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr7:106821200-106851800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr7:106821200-106851800	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr7:106821400-106851800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr7:106821600-106851600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr7:106821600-106851800	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr7:106821800-106847800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr7:106821800-106851400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:106823000-106851200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr7:106823800-106849600	Weak transcription	HMEC	breast
24	chr7:106828600-106849600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:106828600-106851800	Strong transcription	Fetal Intestine Large	intestine
26	chr7:106828800-106849800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr7:106828800-106851200	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr7:106831400-106847800	Weak transcription	Fetal Brain Male	brain
29	chr7:106832000-106852400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr7:106832800-106847800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr7:106833600-106849400	Weak transcription	Esophagus	oesophagus
32	chr7:106834200-106851600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr7:106834800-106851000	Strong transcription	Thymus	Thymus
34	chr7:106835200-106851800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr7:106835400-106852200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:106835600-106848000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr7:106835800-106851000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr7:106835800-106851600	Strong transcription	Fetal Muscle Leg	muscle
39	chr7:106836200-106852000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr7:106836400-106848200	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr7:106836400-106851200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr7:106837000-106851000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr7:106837200-106847800	Strong transcription	Primary hematopoietic stem cells	blood
44	chr7:106837800-106848000	Weak transcription	NHEK	skin
45	chr7:106838000-106847800	Weak transcription	Psoas Muscle	Psoas
46	chr7:106838200-106850600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr7:106838200-106865200	Weak transcription	Stomach Mucosa	stomach
48	chr7:106840000-106853400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr7:106840800-106848400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr7:106841000-106848000	Weak transcription	Muscle Satellite Cultured Cells	--

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