Variant report

Variant	rs724624
Chromosome Location	chr4:27015721-27015722
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	chr4:26858591..26861467-chr4:27014458..27016455,2	K562	blood:

Variant related genes	Relation type
ENSG00000109689	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10006403	0.80[CEU][hapmap]
rs10470822	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs10939144	0.90[ASW][hapmap];0.88[CEU][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs17555311	0.88[CEU][hapmap]
rs4519791	0.92[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap]
rs4692137	0.90[ASW][hapmap];0.88[CEU][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs60006504	0.81[ASN][1000 genomes]
rs6448485	0.84[CEU][hapmap]
rs6448487	0.84[CEU][hapmap]
rs6822297	0.90[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831605	0.84[CEU][hapmap]
rs6847438	0.84[CEU][hapmap]
rs7658174	0.84[CEU][hapmap]
rs7672936	0.92[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap]
rs7692953	0.88[CEU][hapmap]
rs9998368	0.84[CEU][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs724624	STIM2	cis	Whole Blood	GTEx
rs724624	STIM2	cis	uninvolved skin	skin_eQTL
rs724624	STIM2	cis	normal skin	skin_eQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26978400-27019200	Weak transcription	Fetal Intestine Small	intestine
2	chr4:26980400-27019400	Weak transcription	Left Ventricle	heart
3	chr4:26985400-27019400	Weak transcription	Esophagus	oesophagus
4	chr4:26989400-27024800	Weak transcription	Psoas Muscle	Psoas
5	chr4:26989600-27027000	Weak transcription	HepG2	liver
6	chr4:26995000-27019000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:26995000-27028200	Weak transcription	Pancreas	Pancrea
8	chr4:26996400-27026200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:26996600-27018400	Weak transcription	Fetal Intestine Large	intestine
10	chr4:26996600-27019200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:26996800-27019200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:26997400-27019200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr4:27001200-27029600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:27001600-27019000	Weak transcription	Spleen	Spleen
15	chr4:27002000-27019200	Weak transcription	Lung	lung
16	chr4:27002000-27019200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:27002800-27026000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:27004200-27027200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:27004800-27025000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr4:27005000-27018000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:27005000-27019400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:27005400-27017600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:27005600-27019200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr4:27005600-27019600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:27005600-27021800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr4:27005800-27019400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:27005800-27019400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr4:27005800-27019400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr4:27006000-27019200	Weak transcription	HMEC	breast
30	chr4:27006000-27020200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:27006400-27018400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:27006400-27019400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr4:27006400-27024200	Weak transcription	Small Intestine	intestine
34	chr4:27006600-27026000	Weak transcription	Fetal Kidney	kidney
35	chr4:27006800-27016800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:27006800-27019200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:27007000-27025800	Weak transcription	Placenta	Placenta
38	chr4:27007800-27025200	Weak transcription	K562	blood
39	chr4:27007800-27026200	Weak transcription	Gastric	stomach
40	chr4:27008000-27024200	Weak transcription	Brain Substantia Nigra	brain
41	chr4:27008400-27019400	Weak transcription	Brain Angular Gyrus	brain
42	chr4:27008400-27019400	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:27008600-27019200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr4:27009600-27026000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr4:27011400-27016400	Weak transcription	Dnd41	blood
46	chr4:27011400-27017800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:27011400-27018000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:27011400-27018000	Weak transcription	Primary T cells from cord blood	blood
49	chr4:27011400-27018200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:27011400-27019000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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