Variant report

Variant	rs259690
Chromosome Location	chr6:37888035-37888036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:37867448..37869643-chr6:37887668..37889578,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10456096	0.93[CEU][hapmap];0.88[CHB][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10456097	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10807188	0.82[EUR][1000 genomes]
rs1187421	0.85[CEU][hapmap];0.89[CHB][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	0.90[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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214375	0.89[CEU][hapmap]
rs13210701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214465	0.93[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[JPT][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	0.85[CEU][hapmap]
rs2132597	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2395686	0.82[EUR][1000 genomes]
rs259673	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259679	0.80[CEU][hapmap];0.89[CHB][hapmap]
rs259684	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259686	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259689	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];1.00[YRI][hapmap];1.00[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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];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	0.80[CEU][hapmap];0.89[CHB][hapmap]
rs2645102	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][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];0.85[YRI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2645117	0.89[CHB][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	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645131	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.80[EUR][1000 genomes]
rs2645134	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[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	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842529	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34592529	0.87[AFR][1000 genomes]
rs34871463	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35823566	0.84[ASN][1000 genomes]
rs35925070	0.81[AFR][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[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs9394460	1.00[CEU][hapmap];0.88[CHB][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

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37850600-37890400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:37857600-37895400	Weak transcription	Pancreas	Pancrea
3	chr6:37872000-37888200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:37872000-37890400	Weak transcription	Small Intestine	intestine
5	chr6:37872600-37896400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:37873400-37929200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:37874000-37888400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:37874400-37888200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr6:37874600-37903800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:37876600-37903200	Weak transcription	Dnd41	blood
11	chr6:37878800-37900400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:37879600-37889600	Weak transcription	K562	blood
13	chr6:37879800-37890400	Weak transcription	GM12878-XiMat	blood
14	chr6:37880000-37888400	Weak transcription	Gastric	stomach
15	chr6:37880000-37888600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:37880000-37889600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:37880000-37890800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr6:37880000-37892200	Weak transcription	Ovary	ovary
19	chr6:37880000-37896600	Weak transcription	Right Ventricle	heart
20	chr6:37880000-37898000	Weak transcription	Fetal Thymus	thymus
21	chr6:37880200-37888200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr6:37880200-37930000	Weak transcription	Thymus	Thymus
23	chr6:37880400-37889200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr6:37881200-37890200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:37881400-37888200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr6:37881400-37895000	Weak transcription	Left Ventricle	heart
27	chr6:37881400-37896000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr6:37882000-37888200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:37882200-37888600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:37882200-37888600	Weak transcription	Fetal Muscle Leg	muscle
31	chr6:37882400-37888200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr6:37882400-37891800	Weak transcription	Lung	lung
33	chr6:37883000-37888400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:37883400-37888200	Weak transcription	Brain Hippocampus Middle	brain
35	chr6:37883400-37888600	Weak transcription	Fetal Lung	lung
36	chr6:37883600-37888200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:37883600-37888400	Weak transcription	Psoas Muscle	Psoas
38	chr6:37883600-37890800	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr6:37884200-37888800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:37884400-37888200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:37884600-37904800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:37884800-37888200	Weak transcription	Primary T cells from cord blood	blood
43	chr6:37884800-37888200	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr6:37884800-37888400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:37884800-37888400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:37884800-37888400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:37884800-37888400	Weak transcription	HMEC	breast
48	chr6:37884800-37891400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr6:37884800-37891400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:37884800-37895400	Weak transcription	Adipose Nuclei	Adipose

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