Variant report

Variant	rs259689
Chromosome Location	chr6:37890680-37890681
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10456096	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10456097	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10485029	0.87[GIH][hapmap]
rs10807188	0.82[EUR][1000 genomes]
rs1187421	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs1187422	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1187423	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190570	0.89[CHB][hapmap]
rs12192182	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12198907	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200258	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204352	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12206818	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211981	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213835	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214375	0.89[CEU][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs13210701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214465	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13220131	0.84[EUR][1000 genomes]
rs16890277	0.81[ASN][1000 genomes]
rs16890344	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs171831	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1812599	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2055206	0.84[CEU][hapmap]
rs2132597	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2395686	0.82[EUR][1000 genomes]
rs259673	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259679	0.89[CHB][hapmap]
rs259684	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259686	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259695	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259715	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259716	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs259718	0.89[CHB][hapmap]
rs2645102	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2645107	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645113	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645116	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2645117	0.89[CHB][hapmap];1.00[CHD][hapmap]
rs2645120	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2645124	0.86[CHB][hapmap]
rs2645127	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645128	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645131	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs2645134	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes]
rs2645137	0.81[EUR][1000 genomes]
rs2842500	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842517	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842527	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842529	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34871463	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35823566	0.84[ASN][1000 genomes]
rs56098839	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6458027	0.83[EUR][1000 genomes]
rs6458028	0.82[EUR][1000 genomes]
rs6458029	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs6941057	0.81[CEU][hapmap]
rs7747130	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7755089	0.81[EUR][1000 genomes]
rs9296232	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs9394460	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs9647619	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966705	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv970036	chr6:37876765-37894762	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs259689	TAF11	cis	cerebellum	SCAN
rs259689	SLC26A8	cis	cerebellum	SCAN
rs259689	KCNK17	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37857600-37895400	Weak transcription	Pancreas	Pancrea
2	chr6:37872600-37896400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:37873400-37929200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:37874600-37903800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:37876600-37903200	Weak transcription	Dnd41	blood
6	chr6:37878800-37900400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:37880000-37890800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr6:37880000-37892200	Weak transcription	Ovary	ovary
9	chr6:37880000-37896600	Weak transcription	Right Ventricle	heart
10	chr6:37880000-37898000	Weak transcription	Fetal Thymus	thymus
11	chr6:37880200-37930000	Weak transcription	Thymus	Thymus
12	chr6:37881400-37895000	Weak transcription	Left Ventricle	heart
13	chr6:37881400-37896000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:37882400-37891800	Weak transcription	Lung	lung
15	chr6:37883600-37890800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:37884600-37904800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:37884800-37891400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr6:37884800-37891400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:37884800-37895400	Weak transcription	Adipose Nuclei	Adipose
20	chr6:37884800-37898200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr6:37884800-37917000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr6:37885200-37892000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:37885200-37906200	Weak transcription	HSMM	muscle
24	chr6:37885600-37896800	Weak transcription	Fetal Brain Male	brain
25	chr6:37886400-37896400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:37886600-37896600	Weak transcription	Fetal Intestine Small	intestine
27	chr6:37887600-37891400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:37887600-37933200	Weak transcription	NHDF-Ad	bronchial
29	chr6:37887800-37892200	Weak transcription	Spleen	Spleen
30	chr6:37887800-37896400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:37887800-37906200	Weak transcription	HSMMtube	muscle
32	chr6:37887800-37906600	Weak transcription	NH-A	brain
33	chr6:37888200-37891200	Enhancers	Stomach Mucosa	stomach
34	chr6:37888200-37893000	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr6:37888600-37893800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr6:37888600-37893800	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:37888600-37903600	Weak transcription	Osteobl	bone
38	chr6:37888800-37891000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:37888800-37892600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:37888800-37893800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr6:37888800-37893800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr6:37888800-37893800	Weak transcription	Psoas Muscle	Psoas
43	chr6:37888800-37893800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:37888800-37895200	Weak transcription	Right Atrium	heart
45	chr6:37888800-37895400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr6:37888800-37895800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:37888800-37898000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:37888800-37898600	Weak transcription	Fetal Muscle Leg	muscle
49	chr6:37888800-37903800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:37889000-37893600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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