Variant report

Variant	rs10241528
Chromosome Location	chr7:66408980-66408981
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66384580..66387165-chr7:66405669..66409377,3	K562	blood:

Variant related genes	Relation type
ENSG00000106609	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10156059	0.84[EUR][1000 genomes]
rs10224189	0.81[EUR][1000 genomes]
rs10226191	0.81[EUR][1000 genomes]
rs10231411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10232188	0.86[AFR][1000 genomes]
rs10234322	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10234640	0.81[EUR][1000 genomes]
rs10234747	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10235334	0.87[YRI][hapmap];0.89[AFR][1000 genomes]
rs10235423	0.84[AFR][1000 genomes]
rs10235638	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10241395	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs10242870	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10244459	1.00[CEU][hapmap]
rs10245017	0.81[EUR][1000 genomes]
rs10247815	0.83[EUR][1000 genomes]
rs10250124	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10250831	0.86[AFR][1000 genomes]
rs10258628	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10263993	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10264873	0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs10265069	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10266792	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10267253	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10279240	0.89[AFR][1000 genomes]
rs10280816	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10281090	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10282310	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10282522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1060527	1.00[YRI][hapmap]
rs1064795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12532805	0.85[YRI][hapmap]
rs12532829	0.91[AFR][1000 genomes]
rs12532843	0.89[AFR][1000 genomes]
rs12533298	0.89[AFR][1000 genomes]
rs12533724	0.89[AFR][1000 genomes]
rs12534188	0.86[AFR][1000 genomes]
rs12536003	0.94[AFR][1000 genomes]
rs13437994	0.86[EUR][1000 genomes]
rs13438432	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1589887	0.84[AFR][1000 genomes]
rs17138017	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17680606	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs17747927	0.82[EUR][1000 genomes]
rs17748115	0.87[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2013707	0.80[EUR][1000 genomes]
rs2091315	0.85[YRI][hapmap]
rs28460006	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28472679	0.83[EUR][1000 genomes]
rs28501161	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28524571	0.86[AFR][1000 genomes]
rs28560293	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28590087	0.89[AFR][1000 genomes]
rs28641990	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28675035	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3778907	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3778914	0.84[AFR][1000 genomes]
rs3778916	0.87[YRI][hapmap];0.89[AFR][1000 genomes]
rs3800818	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs3823607	0.83[EUR][1000 genomes]
rs3823609	0.87[EUR][1000 genomes]
rs4382352	0.87[YRI][hapmap]
rs4617036	0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs4718417	0.91[EUR][1000 genomes]
rs57774708	0.82[EUR][1000 genomes]
rs57875851	0.81[EUR][1000 genomes]
rs59693594	0.86[EUR][1000 genomes]
rs60026498	0.82[EUR][1000 genomes]
rs60972148	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62465751	0.97[AFR][1000 genomes]
rs62465753	0.94[AFR][1000 genomes]
rs62466579	0.89[AFR][1000 genomes]
rs62466580	0.84[AFR][1000 genomes]
rs67408913	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6965680	0.80[EUR][1000 genomes]
rs71526586	0.84[EUR][1000 genomes]
rs73139941	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73141980	0.81[EUR][1000 genomes]
rs73143921	0.82[EUR][1000 genomes]
rs73143998	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73145911	0.80[EUR][1000 genomes]
rs73145924	0.86[EUR][1000 genomes]
rs73151646	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7455757	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7777631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7785755	0.84[AFR][1000 genomes]
rs7785883	0.85[EUR][1000 genomes]
rs7796977	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7809359	0.83[EUR][1000 genomes]
rs7809535	0.83[EUR][1000 genomes]
rs868960	0.84[EUR][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	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv436556	chr7:66403338-66410081	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10241528	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx
rs10241528	GS1-124K5.12	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66387600-66409800	Weak transcription	Fetal Kidney	kidney
2	chr7:66387600-66428000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:66391200-66409800	Weak transcription	Brain Germinal Matrix	brain
4	chr7:66393400-66411800	Weak transcription	Stomach Mucosa	stomach
5	chr7:66393800-66422200	Weak transcription	Fetal Heart	heart
6	chr7:66395800-66412800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:66396000-66409800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:66396000-66415800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:66398400-66410000	Weak transcription	Right Ventricle	heart
10	chr7:66398800-66409800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr7:66398800-66409800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:66398800-66410000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:66398800-66415400	Weak transcription	Brain Angular Gyrus	brain
14	chr7:66399200-66409600	Weak transcription	Aorta	Aorta
15	chr7:66400600-66426400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:66401800-66409400	Weak transcription	Fetal Lung	lung
17	chr7:66402400-66424200	Strong transcription	Dnd41	blood
18	chr7:66402600-66414000	Strong transcription	Primary T cells from cord blood	blood
19	chr7:66403000-66424800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:66403200-66409800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:66403200-66409800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr7:66403400-66417000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:66403400-66417200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:66403400-66424400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr7:66403400-66426000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr7:66403400-66426400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr7:66403600-66411400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:66403600-66411400	Strong transcription	Duodenum Mucosa	Duodenum
29	chr7:66403600-66417200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr7:66403600-66424600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr7:66403600-66425600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr7:66403600-66426400	Strong transcription	Thymus	Thymus
33	chr7:66403600-66426600	Strong transcription	Fetal Stomach	stomach
34	chr7:66403800-66417200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr7:66403800-66418800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:66403800-66425200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr7:66403800-66425800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr7:66404000-66414000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:66404000-66414000	Strong transcription	K562	blood
40	chr7:66404000-66417400	Strong transcription	Lung	lung
41	chr7:66405000-66424600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr7:66405200-66422800	Strong transcription	Fetal Muscle Leg	muscle
43	chr7:66405400-66409800	Strong transcription	Fetal Intestine Small	intestine
44	chr7:66405400-66410600	Strong transcription	Primary hematopoietic stem cells	blood
45	chr7:66405400-66412800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr7:66405400-66417400	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr7:66405800-66409200	Weak transcription	Brain Hippocampus Middle	brain
48	chr7:66405800-66409800	Weak transcription	Ovary	ovary
49	chr7:66406000-66426400	Strong transcription	Fetal Thymus	thymus
50	chr7:66406200-66421400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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