Variant report

Variant	rs7612605
Chromosome Location	chr3:98562630-98562631
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98561160..98564034-chr3:98567276..98569600,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1062196	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12107050	0.92[EUR][1000 genomes]
rs12330170	0.92[EUR][1000 genomes]
rs12490832	0.92[EUR][1000 genomes]
rs13060012	0.92[EUR][1000 genomes]
rs1440150	0.93[EUR][1000 genomes]
rs1440151	0.91[EUR][1000 genomes]
rs1440152	0.90[EUR][1000 genomes]
rs17270593	0.91[EUR][1000 genomes]
rs1837500	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2119187	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2262597	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2279761	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2334230	0.91[EUR][1000 genomes]
rs2439213	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2439214	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439215	0.83[ASN][1000 genomes]
rs2439217	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2439218	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2439220	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439226	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2439228	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2439229	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2439231	0.85[ASN][1000 genomes]
rs2439236	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2454673	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2454676	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2454677	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2454678	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2454680	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2454682	0.81[ASN][1000 genomes]
rs2454684	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2454685	0.81[ASN][1000 genomes]
rs2454691	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2470857	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2470859	0.81[ASN][1000 genomes]
rs2470860	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2470861	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2470864	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2470865	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2470867	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2470869	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2470879	0.85[ASN][1000 genomes]
rs2470885	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28802000	0.95[EUR][1000 genomes]
rs2919234	0.82[EUR][1000 genomes]
rs2919236	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34234373	0.95[EUR][1000 genomes]
rs34558202	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3755576	0.91[EUR][1000 genomes]
rs3772098	0.90[EUR][1000 genomes]
rs3772099	0.91[EUR][1000 genomes]
rs3772101	0.92[EUR][1000 genomes]
rs3772102	0.91[EUR][1000 genomes]
rs3821359	0.90[EUR][1000 genomes]
rs4269027	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4425201	0.92[EUR][1000 genomes]
rs4426626	0.92[EUR][1000 genomes]
rs4494869	0.92[EUR][1000 genomes]
rs62278486	0.92[EUR][1000 genomes]
rs6785935	0.93[EUR][1000 genomes]
rs6788418	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6790650	0.89[EUR][1000 genomes]
rs6793760	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6808116	0.91[EUR][1000 genomes]
rs704585	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7431448	0.91[EUR][1000 genomes]
rs7611929	0.92[EUR][1000 genomes]
rs7612036	0.92[EUR][1000 genomes]
rs7616275	0.95[EUR][1000 genomes]
rs7630800	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs828609	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs844160	0.91[EUR][1000 genomes]
rs9289683	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9289685	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9811305	0.91[EUR][1000 genomes]
rs9820384	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9845558	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9860216	0.93[EUR][1000 genomes]
rs9866570	0.91[EUR][1000 genomes]
rs9872152	0.91[EUR][1000 genomes]
rs9873932	0.94[EUR][1000 genomes]
rs9878392	0.91[EUR][1000 genomes]
rs9881519	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7612605	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL
rs7612605	DCBLD2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98528200-98575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:98536200-98594200	Weak transcription	HepG2	liver
4	chr3:98537000-98567000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:98537000-98592800	Weak transcription	K562	blood
6	chr3:98538200-98569200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr3:98541200-98567000	Weak transcription	Liver	Liver
8	chr3:98541400-98565000	Weak transcription	HUVEC	blood vessel
9	chr3:98548800-98566600	Weak transcription	Adipose Nuclei	Adipose
10	chr3:98550200-98568600	Weak transcription	Thymus	Thymus
11	chr3:98552600-98566600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:98552600-98567000	Weak transcription	Fetal Kidney	kidney
13	chr3:98552800-98566600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:98552800-98575800	Weak transcription	Pancreas	Pancrea
15	chr3:98552800-98578000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:98552800-98579800	Weak transcription	Right Ventricle	heart
17	chr3:98553000-98563200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:98553000-98565800	Weak transcription	Ovary	ovary
19	chr3:98553000-98566800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:98553000-98566800	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:98553000-98567000	Weak transcription	Brain Germinal Matrix	brain
22	chr3:98553000-98575600	Weak transcription	Fetal Stomach	stomach
23	chr3:98553000-98576000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:98553000-98576200	Weak transcription	Left Ventricle	heart
25	chr3:98553000-98590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:98558200-98566800	Weak transcription	Fetal Thymus	thymus
27	chr3:98558200-98569400	Weak transcription	Fetal Intestine Large	intestine
28	chr3:98558200-98569600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:98558200-98577200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:98558400-98566400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:98558400-98568800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:98558800-98567000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:98559000-98567000	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:98559000-98569000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:98559600-98576800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr3:98559800-98565800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:98559800-98566800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:98559800-98567000	Weak transcription	Dnd41	blood
39	chr3:98559800-98569400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:98560000-98563400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:98560000-98564600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:98560000-98566600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:98560000-98566800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:98560000-98575600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:98560200-98562800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:98560200-98563200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:98560200-98564200	Weak transcription	HMEC	breast
48	chr3:98560200-98566000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:98560200-98566200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr3:98560200-98566800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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