Variant report

Variant	rs10023256
Chromosome Location	chr4:26902361-26902362
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26901193..26903720-chr4:26933025..26935990,2	K562	blood:
2	chr4:26900718..26903532-chr4:26996706..26999074,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10006403	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10029307	0.81[ASW][hapmap]
rs10939144	0.81[CEU][hapmap]
rs11737218	0.81[ASW][hapmap]
rs12331333	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12642608	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs12644073	0.80[ASW][hapmap]
rs12644232	0.80[JPT][hapmap]
rs13434709	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17555311	0.81[CEU][hapmap]
rs4692132	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4692137	0.81[CEU][hapmap]
rs6448478	0.81[JPT][hapmap]
rs6448485	0.85[CEU][hapmap]
rs6448487	0.85[CEU][hapmap]
rs6815719	0.81[ASW][hapmap]
rs6831605	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs6847438	0.85[CEU][hapmap];0.81[JPT][hapmap]
rs7658174	0.85[CEU][hapmap]
rs7678705	0.96[ASN][1000 genomes]
rs7692953	0.82[CEU][hapmap]
rs9654109	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9654110	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9998368	0.85[CEU][hapmap];0.81[JPT][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10023256	STIM2	cis	lymphoblastoid	seeQTL
rs10023256	STIM2	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26875600-26904600	Weak transcription	Brain Anterior Caudate	brain
2	chr4:26880600-26902400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:26880600-26921600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr4:26885800-26903600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:26886600-26921600	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:26889800-26906000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:26894600-26903400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:26897800-26902400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:26898400-26907400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:26898400-26914400	Weak transcription	HSMM	muscle
11	chr4:26899400-26902400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:26899400-26904000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr4:26899400-26905000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr4:26899400-26908000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr4:26899600-26904000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr4:26899600-26904600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:26899800-26902400	Weak transcription	Spleen	Spleen
18	chr4:26899800-26903600	Enhancers	Primary T cells from cord blood	blood
19	chr4:26899800-26903600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr4:26899800-26903600	Weak transcription	Pancreas	Pancrea
21	chr4:26900400-26902400	Weak transcription	Small Intestine	intestine
22	chr4:26900400-26913200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:26900800-26902800	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr4:26900800-26908000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr4:26901000-26903000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:26901200-26902400	Enhancers	HUVEC	blood vessel
27	chr4:26901200-26902800	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr4:26901200-26902800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr4:26901200-26907600	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr4:26901400-26902800	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr4:26901400-26902800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:26901400-26902800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr4:26901400-26903000	Enhancers	Primary B cells from cord blood	blood
34	chr4:26901600-26902600	Enhancers	Brain Hippocampus Middle	brain
35	chr4:26901600-26902600	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr4:26901600-26902800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:26901600-26902800	Enhancers	Adipose Nuclei	Adipose
38	chr4:26901600-26902800	Enhancers	Fetal Lung	lung
39	chr4:26901600-26903000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:26901600-26903000	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr4:26901600-26903600	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr4:26901600-26906800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr4:26901800-26902400	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr4:26901800-26902600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:26901800-26902600	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr4:26901800-26902600	Enhancers	Stomach Mucosa	stomach
47	chr4:26901800-26902600	Enhancers	K562	blood
48	chr4:26901800-26902800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:26901800-26902800	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr4:26901800-26902800	Enhancers	Primary B cells from peripheral blood	blood

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