Variant report

Variant	rs2839686
Chromosome Location	chr10:44881455-44881456
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr10:44881394-44882580	H1-hESC	embryonic stem cell:	n/a	chr10:44882173-44882192 chr10:44882176-44882189 chr10:44882175-44882187 chr10:44882177-44882191 chr10:44882179-44882188

Variant related genes	Relation type
CXCL12	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11239028	0.83[EUR][1000 genomes]
rs11594377	0.82[AFR][1000 genomes]
rs17156287	1.00[ASN][1000 genomes]
rs17482472	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17879548	1.00[ASN][1000 genomes]
rs17880358	1.00[ASN][1000 genomes]
rs17880777	0.87[AFR][1000 genomes]
rs17880863	1.00[ASN][1000 genomes]
rs17881575	1.00[ASN][1000 genomes]
rs17883339	0.98[ASN][1000 genomes]
rs17885289	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197452	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs266088	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs2839679	0.82[AFR][1000 genomes]
rs2839680	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2839682	0.96[ASN][1000 genomes]
rs2839684	0.93[ASN][1000 genomes]
rs2839687	0.86[AFR][1000 genomes]
rs2839689	0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs2839690	0.90[LWK][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs2839692	0.90[LWK][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs2839695	0.90[LWK][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs2861441	0.82[AFR][1000 genomes]
rs2861442	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3780891	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7082547	0.82[AFR][1000 genomes]
rs7088876	0.86[AFR][1000 genomes]
rs7092453	0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs7093481	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790861	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728142	0.96[ASN][1000 genomes]
rs7915848	0.90[LWK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054649	chr10:44848921-44889713	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv550699	chr10:44868257-44882203	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv895090	chr10:44874867-44884959	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv895091	chr10:44875040-44888130	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv895092	chr10:44875166-44884959	Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv895093	chr10:44876461-44884959	Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv895094	chr10:44876499-44884959	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv895095	chr10:44876586-44884959	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv895096	chr10:44876586-44886206	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv895097	chr10:44876586-44888130	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv550700	chr10:44878064-44882203	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	nsv895099	chr10:44878114-44884959	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	nsv895100	chr10:44878835-44884959	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
14	esv3375268	chr10:44878846-44883969	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
15	esv3421241	chr10:44879371-44881919	Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2839686	SYT15	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44878600-44881600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
2	chr10:44878800-44881800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr10:44879000-44882400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr10:44879400-44882600	Bivalent Enhancer	Fetal Brain Male	brain
5	chr10:44879600-44881600	Active TSS	Osteobl	bone
6	chr10:44879600-44882400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr10:44879800-44882200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr10:44880000-44882400	Bivalent/Poised TSS	Fetal Brain Female	brain
9	chr10:44880200-44881800	Bivalent Enhancer	Placenta	Placenta
10	chr10:44880200-44882600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:44880400-44881600	Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr10:44880400-44881800	Bivalent/Poised TSS	Colonic Mucosa	Colon
13	chr10:44880400-44881800	Bivalent Enhancer	Spleen	Spleen
14	chr10:44880600-44881600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr10:44880600-44881600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
16	chr10:44880800-44881600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr10:44880800-44881600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
18	chr10:44880800-44881800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
19	chr10:44880800-44881800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr10:44880800-44881800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
21	chr10:44880800-44881800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
22	chr10:44880800-44881800	Bivalent Enhancer	Stomach Mucosa	stomach
23	chr10:44881000-44881600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
24	chr10:44881000-44881600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr10:44881000-44881600	Bivalent Enhancer	Fetal Intestine Large	intestine
26	chr10:44881000-44881800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
27	chr10:44881000-44881800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
28	chr10:44881000-44882200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr10:44881000-44882600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
30	chr10:44881000-44884600	Weak transcription	Psoas Muscle	Psoas
31	chr10:44881000-44884600	Weak transcription	NHDF-Ad	bronchial
32	chr10:44881200-44881600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr10:44881200-44881600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
34	chr10:44881200-44881600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
35	chr10:44881200-44881600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
36	chr10:44881200-44881600	Bivalent Enhancer	Fetal Heart	heart
37	chr10:44881200-44881600	Weak transcription	Right Ventricle	heart
38	chr10:44881200-44881800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr10:44881200-44881800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
40	chr10:44881200-44881800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr10:44881200-44881800	Bivalent Enhancer	Fetal Intestine Small	intestine
42	chr10:44881200-44882200	Weak transcription	Ovary	ovary
43	chr10:44881200-44882200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr10:44881200-44882400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr10:44881200-44882600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
46	chr10:44881200-44884200	Weak transcription	Liver	Liver
47	chr10:44881200-44884200	Weak transcription	Right Atrium	heart
48	chr10:44881200-44884400	Weak transcription	Left Ventricle	heart
49	chr10:44881400-44881600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
50	chr10:44881400-44881600	Bivalent Enhancer	Stomach Smooth Muscle	stomach

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