Variant report

Variant	rs12055836
Chromosome Location	chr6:45899823-45899824
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12662995	0.89[AMR][1000 genomes]
rs3777566	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777574	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs3777575	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs3777578	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes]
rs3798263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3798266	1.00[CEU][hapmap]
rs3822886	0.89[AMR][1000 genomes]
rs6907979	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs9357496	0.89[AMR][1000 genomes]
rs9395137	0.84[AMR][1000 genomes]
rs946226	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs949678	1.00[CEU][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv517891	chr6:45899823-45915088	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12055836	SOCS2	trans	brain	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45881200-45908000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:45886800-45910600	Weak transcription	Psoas Muscle	Psoas
3	chr6:45890600-45901600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:45895400-45910800	Weak transcription	Placenta	Placenta
5	chr6:45896200-45901400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:45897800-45901400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:45898200-45901600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:45898200-45904400	Weak transcription	Spleen	Spleen
9	chr6:45898600-45901200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:45898600-45901400	Weak transcription	Osteobl	bone
11	chr6:45898600-45914600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:45898600-45916800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:45898800-45900400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:45898800-45903400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:45898800-45904200	Weak transcription	Colonic Mucosa	Colon
16	chr6:45898800-45911000	Weak transcription	Adipose Nuclei	Adipose
17	chr6:45898800-45919200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:45899000-45900600	Weak transcription	Fetal Intestine Large	intestine
19	chr6:45899000-45910600	Weak transcription	Fetal Heart	heart
20	chr6:45899200-45900200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:45899200-45900200	Weak transcription	Right Ventricle	heart
22	chr6:45899200-45900200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr6:45899200-45901400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:45899200-45901400	Weak transcription	Fetal Kidney	kidney
25	chr6:45899200-45910000	Strong transcription	Fetal Intestine Small	intestine
26	chr6:45899400-45905400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr6:45899600-45902000	Strong transcription	Left Ventricle	heart
28	chr6:45899800-45908000	Weak transcription	Lung	lung

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