Variant report

Variant	rs12209616
Chromosome Location	chr6:166735173-166735174
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:166733862..166736433-chr6:166795444..166796980,2	K562	blood:

Variant related genes	Relation type
ENSG00000261420	Chromatin interaction
ENSG00000060762	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10455809	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10455976	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10455977	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10455978	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10946152	0.89[EUR][1000 genomes]
rs10946158	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10946160	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10946161	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11551053	0.84[ASN][1000 genomes]
rs11752886	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11753652	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11755305	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12198613	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12214281	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12214812	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12662920	0.82[EUR][1000 genomes]
rs12662924	0.90[EUR][1000 genomes]
rs1599841	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1830558	0.88[ASN][1000 genomes]
rs2294333	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2294334	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2294335	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4144886	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4144887	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4144888	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4709111	0.84[ASN][1000 genomes]
rs4710042	0.84[ASN][1000 genomes]
rs55936781	0.88[EUR][1000 genomes]
rs59337176	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66461381	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68016351	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7088	0.87[ASN][1000 genomes]
rs73030701	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73263155	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73788236	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740965	0.81[EUR][1000 genomes]
rs7753161	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7771603	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs927190	0.86[ASN][1000 genomes]
rs9347123	0.87[ASN][1000 genomes]
rs9348119	0.87[ASN][1000 genomes]
rs9348121	0.85[ASN][1000 genomes]
rs9355571	0.88[ASN][1000 genomes]
rs9366004	0.88[ASN][1000 genomes]
rs941683	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886934	chr6:166642850-166747572	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12209616	SFT2D1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166722600-166735600	Weak transcription	Brain Angular Gyrus	brain
2	chr6:166723200-166735400	Weak transcription	Brain Substantia Nigra	brain
3	chr6:166723200-166735600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:166723200-166738800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:166723200-166744200	Weak transcription	Right Atrium	heart
6	chr6:166723600-166735800	Weak transcription	Brain Anterior Caudate	brain
7	chr6:166723800-166736000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:166727400-166736400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:166727400-166739000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:166727600-166736400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:166727800-166736200	Weak transcription	Fetal Lung	lung
12	chr6:166728000-166735800	Weak transcription	NHLF	lung
13	chr6:166728400-166736400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:166728600-166735800	Weak transcription	Ovary	ovary
15	chr6:166728600-166736400	Weak transcription	NHDF-Ad	bronchial
16	chr6:166728600-166737800	Weak transcription	Brain Germinal Matrix	brain
17	chr6:166729000-166745400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:166729200-166744200	Weak transcription	Stomach Mucosa	stomach
19	chr6:166729600-166735800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:166729600-166744000	Weak transcription	Small Intestine	intestine
21	chr6:166730400-166736200	Weak transcription	NH-A	brain
22	chr6:166730400-166740600	Weak transcription	Fetal Kidney	kidney
23	chr6:166730400-166744200	Weak transcription	Fetal Brain Male	brain
24	chr6:166730600-166739000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:166730800-166736600	Weak transcription	NHEK	skin
26	chr6:166730800-166739000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:166731000-166736400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr6:166731200-166735400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:166731400-166739000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr6:166731400-166742800	Strong transcription	Fetal Intestine Small	intestine
31	chr6:166731400-166742800	Strong transcription	Fetal Stomach	stomach
32	chr6:166731600-166736200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:166731600-166739000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:166731600-166743000	Strong transcription	Thymus	Thymus
35	chr6:166731800-166738400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:166731800-166739000	Weak transcription	A549	lung
37	chr6:166731800-166742600	Strong transcription	Placenta	Placenta
38	chr6:166731800-166742800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr6:166731800-166743000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:166731800-166743000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:166731800-166743400	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr6:166732000-166738400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:166732000-166740200	Strong transcription	Fetal Brain Female	brain
44	chr6:166732000-166742800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr6:166732000-166743000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:166732200-166736400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:166732200-166743000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:166732200-166743000	Strong transcription	Fetal Thymus	thymus
49	chr6:166732200-166743000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr6:166732400-166737600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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