Variant report

Variant	rs6855865
Chromosome Location	chr4:27011357-27011358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10007132	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs10010180	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs10019691	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10030655	0.82[CHB][hapmap]
rs1012550	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10470823	0.82[CHB][hapmap]
rs10939147	0.91[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1122045	0.82[CHB][hapmap]
rs12152700	0.95[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12331378	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13115054	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs13127603	0.82[CHB][hapmap]
rs13140015	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16878653	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs16878671	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28572642	0.82[ASN][1000 genomes]
rs28668622	0.87[EUR][1000 genomes]
rs2871256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3762900	0.91[ASW][hapmap];0.95[CEU][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4692136	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6830950	0.82[TSI][hapmap]
rs6833149	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6838936	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6856381	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7669818	0.84[EUR][1000 genomes]
rs7679403	0.92[AFR][1000 genomes]
rs7681802	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7693687	0.91[ASW][hapmap];0.96[YRI][hapmap]
rs7695335	0.80[CEU][hapmap]
rs7700108	0.90[CEU][hapmap];0.90[AFR][1000 genomes]
rs9291487	0.95[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs9998009	0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.96[ASN][1000 genomes]
rs9998971	0.91[AFR][1000 genomes];0.84[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	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
rs6855865	STIM2	cis	uninvolved skin	skin_eQTL
rs6855865	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs6855865	STIM2	cis	normal skin	skin_eQTL

Chromatin state (count:102 , 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	chr4:26996200-27015400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:26996400-27026200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:26996600-27011800	Weak transcription	Brain Anterior Caudate	brain
11	chr4:26996600-27018400	Weak transcription	Fetal Intestine Large	intestine
12	chr4:26996600-27019200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:26996800-27019200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:26997400-27019200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr4:27001200-27029600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:27001600-27019000	Weak transcription	Spleen	Spleen
17	chr4:27002000-27019200	Weak transcription	Lung	lung
18	chr4:27002000-27019200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:27002200-27013000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr4:27002800-27011800	Weak transcription	Stomach Mucosa	stomach
21	chr4:27002800-27026000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:27003400-27011600	Strong transcription	Primary B cells from cord blood	blood
23	chr4:27004200-27027200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:27004800-27025000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:27005000-27018000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:27005000-27019400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:27005400-27011800	Enhancers	Osteobl	bone
28	chr4:27005400-27017600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:27005600-27012000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:27005600-27013400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:27005600-27019200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr4:27005600-27019600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:27005600-27021800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr4:27005800-27019400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:27005800-27019400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr4:27005800-27019400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr4:27006000-27019200	Weak transcription	HMEC	breast
38	chr4:27006000-27020200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:27006400-27018400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:27006400-27019400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr4:27006400-27024200	Weak transcription	Small Intestine	intestine
42	chr4:27006600-27026000	Weak transcription	Fetal Kidney	kidney
43	chr4:27006800-27016800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:27006800-27019200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:27007000-27025800	Weak transcription	Placenta	Placenta
46	chr4:27007800-27011600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr4:27007800-27025200	Weak transcription	K562	blood
48	chr4:27007800-27026200	Weak transcription	Gastric	stomach
49	chr4:27008000-27024200	Weak transcription	Brain Substantia Nigra	brain
50	chr4:27008200-27012400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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