Variant report

Variant	rs3823609
Chromosome Location	chr7:66265028-66265029
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	chr7:66264090..66265876-chr7:66269998..66272593,2	K562	blood:
2	chr7:66258319..66260099-chr7:66263476..66266202,2	K562	blood:

Extended variants
information (count: 101 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10224536	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10225392	0.81[EUR][1000 genomes]
rs10228381	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs10229580	0.81[EUR][1000 genomes]
rs10231411	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10231860	0.83[EUR][1000 genomes]
rs10234322	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10234747	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10235037	0.83[EUR][1000 genomes]
rs10235423	0.84[TSI][hapmap];0.88[YRI][hapmap]
rs10235638	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10237244	0.83[EUR][1000 genomes]
rs10240153	0.81[EUR][1000 genomes]
rs10240582	0.81[EUR][1000 genomes]
rs10241395	1.00[CEU][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes]
rs10241528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs10242870	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10243608	0.84[EUR][1000 genomes]
rs10244459	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10247324	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10250124	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10252133	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10256117	0.82[EUR][1000 genomes]
rs10257393	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10258628	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10262184	0.80[ASN][1000 genomes]
rs10263993	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10264873	0.84[TSI][hapmap]
rs10265069	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10267253	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10267834	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10267922	0.88[YRI][hapmap]
rs10270326	0.82[EUR][1000 genomes]
rs10271177	0.81[EUR][1000 genomes]
rs10273320	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10278343	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10281090	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10282310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10282522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10479728	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1060527	0.87[YRI][hapmap];0.88[EUR][1000 genomes]
rs1064795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12234826	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12333749	0.81[EUR][1000 genomes]
rs12334214	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12532805	0.84[TSI][hapmap]
rs12534188	0.84[TSI][hapmap]
rs12534948	0.84[TSI][hapmap]
rs13437901	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13438432	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1589887	0.88[YRI][hapmap]
rs17138017	0.85[YRI][hapmap]
rs17138274	1.00[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs17680606	0.84[TSI][hapmap];0.87[YRI][hapmap]
rs17680708	0.86[TSI][hapmap]
rs17748115	0.88[CEU][hapmap];0.82[YRI][hapmap]
rs17748222	0.91[TSI][hapmap]
rs1882656	1.00[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap]
rs1882657	1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap]
rs2013707	0.85[EUR][1000 genomes]
rs2091315	0.82[CHB][hapmap];0.85[YRI][hapmap]
rs28368585	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28375318	0.83[EUR][1000 genomes]
rs28379824	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs28460006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28533332	0.88[EUR][1000 genomes]
rs28547918	0.87[EUR][1000 genomes]
rs28560293	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28607736	0.82[EUR][1000 genomes]
rs28634091	0.89[EUR][1000 genomes]
rs28663128	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs28675035	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs3764904	1.00[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap]
rs3778907	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778908	0.88[EUR][1000 genomes]
rs3778914	0.84[TSI][hapmap];0.88[YRI][hapmap]
rs3800814	0.89[EUR][1000 genomes]
rs3800818	1.00[CEU][hapmap]
rs3823607	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3962133	0.84[EUR][1000 genomes]
rs4617036	0.84[TSI][hapmap]
rs4718417	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60972148	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67408913	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6971508	0.91[TSI][hapmap]
rs6973897	0.81[EUR][1000 genomes]
rs6974601	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73133851	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73135960	0.81[EUR][1000 genomes]
rs73137960	0.82[EUR][1000 genomes]
rs73137963	0.81[EUR][1000 genomes]
rs73139941	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73139976	0.84[EUR][1000 genomes]
rs73143998	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7455757	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7777631	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7785755	0.88[YRI][hapmap]
rs7796977	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[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	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3823609	GS1-124K5.12	cis	Skin Sun Exposed Lower leg	GTEx
rs3823609	CRCP	cis	parietal	SCAN
rs3823609	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx
rs3823609	GUSB	cis	cerebellum	SCAN
rs3823609	ZNF273	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66232600-66279800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:66234800-66275800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:66236800-66265200	Strong transcription	Primary B cells from peripheral blood	blood
4	chr7:66236800-66276800	Strong transcription	Dnd41	blood
5	chr7:66236800-66277000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr7:66236800-66278400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr7:66237200-66277600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:66238200-66276600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr7:66245600-66279200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:66245600-66279400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr7:66246200-66277800	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr7:66246200-66279800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:66248400-66277800	Strong transcription	Osteobl	bone
14	chr7:66248600-66276800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr7:66248800-66277600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr7:66249400-66278600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:66250000-66279200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr7:66250000-66279200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr7:66250200-66277800	Strong transcription	Primary T cells from cord blood	blood
20	chr7:66250200-66278600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr7:66253200-66277600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:66254000-66277400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:66254000-66278400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:66254200-66276000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:66254200-66277200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr7:66254200-66278600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr7:66254600-66278600	Strong transcription	HSMM	muscle
28	chr7:66254800-66267400	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr7:66254800-66268600	Strong transcription	GM12878-XiMat	blood
30	chr7:66254800-66275800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:66254800-66276200	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr7:66254800-66276800	Strong transcription	Stomach Smooth Muscle	stomach
33	chr7:66254800-66276800	Strong transcription	HepG2	liver
34	chr7:66254800-66277800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr7:66255200-66267400	Strong transcription	Brain Cingulate Gyrus	brain
36	chr7:66255200-66268600	Strong transcription	Brain Anterior Caudate	brain
37	chr7:66255200-66277000	Strong transcription	HMEC	breast
38	chr7:66255600-66277200	Weak transcription	Fetal Heart	heart
39	chr7:66255600-66279800	Weak transcription	Right Atrium	heart
40	chr7:66256200-66278600	Strong transcription	Adipose Nuclei	Adipose
41	chr7:66256600-66272400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr7:66256600-66278400	Strong transcription	Fetal Muscle Leg	muscle
43	chr7:66256600-66278600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr7:66256600-66279000	Strong transcription	Fetal Stomach	stomach
45	chr7:66257000-66276800	Strong transcription	Fetal Intestine Large	intestine
46	chr7:66257200-66277800	Strong transcription	Ovary	ovary
47	chr7:66257200-66278400	Strong transcription	Thymus	Thymus
48	chr7:66257600-66278600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr7:66258200-66267200	Strong transcription	Primary hematopoietic stem cells	blood
50	chr7:66258400-66277000	Strong transcription	HUES6 Cell Line	embryonic stem cell

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