Variant report

Variant	rs13127603
Chromosome Location	chr4:26920267-26920268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26917818..26920281-chr4:26922322..26924657,2	MCF-7	breast:
2	chr4:26858949..26860888-chr4:26918795..26920351,2	K562	blood:

Variant related genes	Relation type
ENSG00000109689	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10004120	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10007132	0.90[CEU][hapmap]
rs10014701	0.82[ASN][1000 genomes]
rs10022599	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10030655	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10213674	0.84[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs10433805	0.86[CEU][hapmap]
rs10470823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10939140	0.81[EUR][1000 genomes]
rs10939141	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10939143	0.89[EUR][1000 genomes]
rs1122045	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722221	0.85[CEU][hapmap];0.84[CHB][hapmap];0.84[JPT][hapmap]
rs11722323	0.86[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap]
rs11727649	0.81[CEU][hapmap]
rs12331378	0.90[CEU][hapmap];0.85[CHB][hapmap]
rs12505133	0.81[CEU][hapmap]
rs13114545	0.86[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.83[TSI][hapmap]
rs13115054	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs13147585	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13152367	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28600019	0.81[ASN][1000 genomes]
rs2871256	0.82[CHB][hapmap]
rs34506340	0.84[ASN][1000 genomes]
rs4586918	0.81[CEU][hapmap]
rs4692136	0.90[CEU][hapmap];0.82[CHB][hapmap]
rs6830016	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6830950	1.00[ASW][hapmap];0.86[CEU][hapmap]
rs6855865	0.82[CHB][hapmap]
rs7655631	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs7693687	0.86[CEU][hapmap]
rs7695335	0.85[CEU][hapmap]
rs9998009	0.85[CEU][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap]

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	nsv470021	chr4:26721578-27067027	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1001306	chr4:26821511-26955344	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv461312	chr4:26844674-27078376	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv593872	chr4:26844674-27078376	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1000568	chr4:26886920-27049554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13127603	C4orf52	cis	parietal	SCAN
rs13127603	STIM2	cis	lymphoblastoid	seeQTL
rs13127603	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs13127603	STIM2	cis	multi-tissue	Pritchard

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26880600-26921600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:26886600-26921600	Weak transcription	Fetal Muscle Leg	muscle
3	chr4:26907200-26937800	Weak transcription	Stomach Mucosa	stomach
4	chr4:26909600-26921400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:26909600-26923000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:26909800-26921400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:26910000-26926600	Weak transcription	Fetal Stomach	stomach
8	chr4:26910200-26921000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr4:26910200-26921000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr4:26910200-26921200	Weak transcription	Primary B cells from cord blood	blood
11	chr4:26910200-26925800	Weak transcription	NHEK	skin
12	chr4:26910400-26921400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:26910800-26921800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr4:26911600-26965800	Weak transcription	HMEC	breast
15	chr4:26912600-26921600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr4:26914000-26923000	Weak transcription	Aorta	Aorta
17	chr4:26914200-26924200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:26914600-26921000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:26914600-26921600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:26914600-26921600	Weak transcription	Fetal Intestine Large	intestine
21	chr4:26914600-26921600	Weak transcription	Thymus	Thymus
22	chr4:26914600-26921800	Weak transcription	Fetal Brain Male	brain
23	chr4:26914600-26924800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr4:26914600-26936800	Weak transcription	Small Intestine	intestine
25	chr4:26914800-26921000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:26914800-26921000	Weak transcription	GM12878-XiMat	blood
27	chr4:26914800-26921200	Weak transcription	Adipose Nuclei	Adipose
28	chr4:26914800-26921200	Weak transcription	HSMM	muscle
29	chr4:26914800-26921400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr4:26914800-26921400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr4:26914800-26921600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:26914800-26921600	Weak transcription	Left Ventricle	heart
33	chr4:26914800-26921800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:26914800-26923400	Weak transcription	NHDF-Ad	bronchial
35	chr4:26914800-26924800	Weak transcription	Lung	lung
36	chr4:26914800-26925200	Weak transcription	NHLF	lung
37	chr4:26914800-26925800	Weak transcription	Colonic Mucosa	Colon
38	chr4:26914800-26926000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr4:26914800-26929200	Weak transcription	K562	blood
40	chr4:26914800-26929600	Weak transcription	Pancreas	Pancrea
41	chr4:26914800-26930000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr4:26914800-26932400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr4:26914800-26932600	Weak transcription	Spleen	Spleen
44	chr4:26914800-26942200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:26915000-26921200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr4:26915200-26921600	Weak transcription	Duodenum Mucosa	Duodenum
47	chr4:26915800-26924200	Weak transcription	Fetal Intestine Small	intestine
48	chr4:26917200-26921000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr4:26917200-26921400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:26917600-26921200	Weak transcription	Primary T cells fromperipheralblood	blood

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