Variant report

Variant	rs7672936
Chromosome Location	chr4:26884408-26884409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:26879279..26881991-chr4:26883787..26885649,2	K562	blood:
2	chr4:26876702..26878634-chr4:26883669..26885455,2	K562	blood:
3	chr4:26877548..26879443-chr4:26882952..26885822,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10002654	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10006403	0.85[CEU][hapmap]
rs10470822	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10939144	0.89[CEU][hapmap]
rs12331333	0.81[CEU][hapmap]
rs12644232	0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs13129075	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17555311	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs28445387	0.95[ASN][1000 genomes]
rs28454570	0.82[EUR][1000 genomes]
rs28704572	0.82[EUR][1000 genomes]
rs4133239	0.93[ASN][1000 genomes]
rs4519791	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4692128	0.93[ASN][1000 genomes]
rs4692129	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[ASN][1000 genomes]
rs4692131	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4692137	0.89[CEU][hapmap]
rs6448485	0.92[CEU][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6448487	0.92[CEU][hapmap]
rs6822297	0.92[CEU][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap]
rs6830323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6831605	0.92[CEU][hapmap];0.82[YRI][hapmap]
rs6847438	0.92[CEU][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs724624	0.92[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap]
rs725981	0.92[ASW][hapmap];0.81[CEU][hapmap];0.82[MEX][hapmap]
rs7658174	0.92[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7666651	0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs7678576	0.90[ASN][1000 genomes]
rs7688788	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7692953	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs7697626	0.90[ASN][1000 genomes]
rs9998368	0.93[ASW][hapmap];0.92[CEU][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7672936	STIM2	cis	cerebellum	SCAN
rs7672936	STIM2	cis	Whole Blood	GTEx
rs7672936	STIM2	cis	uninvolved skin	skin_eQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26864400-26886600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr4:26864600-26885600	Weak transcription	Thymus	Thymus
3	chr4:26869800-26886000	Weak transcription	Fetal Stomach	stomach
4	chr4:26873000-26886200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr4:26875600-26904600	Weak transcription	Brain Anterior Caudate	brain
6	chr4:26875800-26888200	Weak transcription	Adipose Nuclei	Adipose
7	chr4:26876400-26885600	Weak transcription	Fetal Lung	lung
8	chr4:26878000-26885400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:26878600-26885600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr4:26878600-26885800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr4:26879200-26885400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr4:26879200-26885400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr4:26880200-26885000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:26880200-26885000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:26880200-26885600	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr4:26880600-26884800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr4:26880600-26885600	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:26880600-26902400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:26880600-26921600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:26880800-26885200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:26881400-26885600	Enhancers	Primary B cells from peripheral blood	blood
22	chr4:26881800-26885200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:26881800-26885600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:26881800-26886800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:26881800-26896200	Weak transcription	HMEC	breast
26	chr4:26882000-26885000	Weak transcription	Fetal Heart	heart
27	chr4:26882000-26885400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr4:26882000-26885400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:26882000-26885400	Weak transcription	Small Intestine	intestine
30	chr4:26882000-26885800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr4:26882000-26887800	Weak transcription	Stomach Mucosa	stomach
32	chr4:26882000-26897000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:26882200-26889000	Weak transcription	K562	blood
34	chr4:26882600-26885800	Enhancers	Primary T cells fromperipheralblood	blood
35	chr4:26883000-26885200	Enhancers	Primary B cells from cord blood	blood
36	chr4:26883000-26885800	Weak transcription	Brain Substantia Nigra	brain
37	chr4:26883200-26885400	Enhancers	GM12878-XiMat	blood
38	chr4:26883200-26885600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr4:26883400-26892800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr4:26883600-26887200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:26883800-26885600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:26883800-26885800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr4:26884200-26884600	Weak transcription	Primary T cells from cord blood	blood
44	chr4:26884200-26884600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:26884200-26884600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr4:26884200-26885400	Enhancers	Dnd41	blood
47	chr4:26884200-26885800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr4:26884200-26886400	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr4:26884200-26886400	Weak transcription	Brain Hippocampus Middle	brain
50	chr4:26884400-26884800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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