Variant report

Variant	rs7679403
Chromosome Location	chr4:26994144-26994145
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26992638..26994590-chr4:27000990..27003803,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10010180	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10019691	0.93[AFR][1000 genomes]
rs10433805	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12152700	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13140015	0.87[EUR][1000 genomes]
rs16878671	0.95[AFR][1000 genomes]
rs28570016	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28668622	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2871258	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35499018	0.99[ASN][1000 genomes]
rs3762900	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4692136	0.85[EUR][1000 genomes]
rs4692142	0.83[ASN][1000 genomes]
rs6448491	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6830950	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833149	0.91[AFR][1000 genomes]
rs6838936	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6855865	0.92[AFR][1000 genomes]
rs6856381	0.91[AFR][1000 genomes]
rs7669818	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7680613	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7681802	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7693687	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7695335	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7700108	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9291487	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9995206	0.81[AMR][1000 genomes]
rs9998971	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7679403	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26963600-26994200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:26966600-26994600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:26975800-27003200	Weak transcription	Aorta	Aorta
4	chr4:26978000-26994600	Weak transcription	Fetal Stomach	stomach
5	chr4:26978400-27019200	Weak transcription	Fetal Intestine Small	intestine
6	chr4:26980400-26994800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:26980400-27019400	Weak transcription	Left Ventricle	heart
8	chr4:26985400-27019400	Weak transcription	Esophagus	oesophagus
9	chr4:26986000-26994400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:26986200-26994400	Weak transcription	Right Atrium	heart
11	chr4:26986400-26994600	Weak transcription	Small Intestine	intestine
12	chr4:26988400-26994600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:26988400-26998000	Weak transcription	Dnd41	blood
14	chr4:26989000-26994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:26989000-26994400	Weak transcription	HSMM	muscle
16	chr4:26989000-27010000	Weak transcription	Thymus	Thymus
17	chr4:26989000-27010400	Weak transcription	Fetal Thymus	thymus
18	chr4:26989200-26994600	Weak transcription	Pancreas	Pancrea
19	chr4:26989400-26994200	Weak transcription	HSMMtube	muscle
20	chr4:26989400-26994600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:26989400-26996000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:26989400-26997000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:26989400-27024800	Weak transcription	Psoas Muscle	Psoas
24	chr4:26989600-27027000	Weak transcription	HepG2	liver
25	chr4:26992600-26994200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:26993200-26994200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr4:26993200-26995000	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr4:26993200-26996800	Enhancers	Fetal Lung	lung
29	chr4:26993200-26997000	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr4:26993200-26997200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr4:26993400-26995200	Weak transcription	Brain Germinal Matrix	brain
32	chr4:26993400-26995400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr4:26993400-26996000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:26993400-26996200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr4:26993400-26996800	Enhancers	Colon Smooth Muscle	Colon
36	chr4:26993400-26997000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr4:26993400-26997000	Enhancers	Brain Hippocampus Middle	brain
38	chr4:26993400-26997200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:26993400-26997200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr4:26993400-26997200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:26993400-26997400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr4:26993400-26997800	Enhancers	Primary T cells from cord blood	blood
43	chr4:26993600-26994600	Weak transcription	Ovary	ovary
44	chr4:26993800-26994200	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr4:26993800-26994400	Enhancers	Fetal Heart	heart
46	chr4:26993800-26994600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:26993800-26996600	Enhancers	Brain Anterior Caudate	brain
48	chr4:26994000-26994200	Enhancers	Primary T cells fromperipheralblood	blood
49	chr4:26994000-26994200	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr4:26994000-26994400	Flanking Active TSS	GM12878-XiMat	blood

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