Variant report

Variant	rs3755597
Chromosome Location	chr3:99356614-99356615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr3:99356350-99357696	H1-hESC	embryonic stem cell:	n/a	chr3:99356873-99356882 chr3:99356825-99356836
2	POLR2A	chr3:99355815-99360014	HUVEC	blood vessel:	n/a	n/a
3	MYC	chr3:99356494-99356730	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:99356140-99356911	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr3:99356314-99356624	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:99355631-99357863	U87	brain:	n/a	n/a
7	POLR2A	chr3:99355828-99358032	IMR90	lung:	n/a	n/a
8	POLR2A	chr3:99355628-99358881	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr3:99356573-99357805	Gliobla	brain:	n/a	n/a
10	STAT3	chr3:99356100-99356672	MCF10A-Er-Src	breast:	n/a	chr3:99356261-99356273 chr3:99356236-99356243 chr3:99356249-99356261
11	FOSL2	chr3:99355978-99356674	SK-N-SH	brain:	n/a	chr3:99356376-99356386 chr3:99356376-99356386 chr3:99356376-99356386 chr3:99356377-99356386 chr3:99356376-99356386
12	POLR2A	chr3:99356017-99357895	HUVEC	blood vessel:	n/a	n/a
13	RCOR1	chr3:99356234-99356637	Hela-S3	cervix:	n/a	n/a
14	CTBP2	chr3:99356391-99357664	H1-hESC	embryonic stem cell:	n/a	n/a
15	RAD21	chr3:99355848-99356742	IMR90	lung:	n/a	chr3:99356571-99356583 chr3:99356570-99356579 chr3:99356571-99356581
16	STAT3	chr3:99355986-99356684	MCF10A-Er-Src	breast:	n/a	chr3:99356261-99356273 chr3:99356236-99356243 chr3:99356249-99356261
17	POLR2A	chr3:99355570-99359960	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr3:99356148-99361614	ProgFib	skin:	n/a	n/a
19	E2F4	chr3:99355971-99356638	MCF10A-Er-Src	breast:	n/a	n/a
20	JUND	chr3:99356055-99356660	SK-N-SH	brain:	n/a	chr3:99356376-99356386 chr3:99356376-99356386 chr3:99356376-99356386 chr3:99356377-99356386 chr3:99356376-99356386
21	CEBPB	chr3:99356452-99356707	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr3:99355795-99356914	H1-neurons	neurons:	n/a	n/a
23	POLR2A	chr3:99355587-99364509	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr3:99355926-99356712	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr3:99355814-99356803	U87	brain:	n/a	n/a
26	POLR2A	chr3:99355625-99357886	U87	brain:	n/a	n/a
27	POLR2A	chr3:99356087-99356840	U87	brain:	n/a	n/a
28	JUND	chr3:99355839-99356803	SK-N-SH	brain:	n/a	chr3:99356376-99356386 chr3:99356376-99356386 chr3:99356376-99356386 chr3:99356377-99356386 chr3:99356376-99356386
29	JUND	chr3:99356037-99356648	Hela-S3	cervix:	n/a	chr3:99356376-99356386 chr3:99356376-99356386 chr3:99356376-99356386 chr3:99356377-99356386 chr3:99356376-99356386
30	MYC	chr3:99356397-99356665	MCF10A-Er-Src	breast:	n/a	n/a
31	FOS	chr3:99355913-99356727	HUVEC	blood vessel:	n/a	chr3:99356376-99356386 chr3:99356376-99356386 chr3:99356375-99356386 chr3:99356376-99356386 chr3:99356377-99356386 chr3:99356376-99356386
32	POLR2A	chr3:99355776-99359911	MCF10A-Er-Src	breast:	n/a	n/a
33	JUND	chr3:99355966-99356738	SK-N-SH	brain:	n/a	chr3:99356376-99356386 chr3:99356376-99356386 chr3:99356376-99356386 chr3:99356377-99356386 chr3:99356376-99356386

Variant related genes	Relation type
COL8A1	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1567784	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16841561	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16841568	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1818482	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3732447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3755596	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928205	0.96[EUR][1000 genomes]
rs4928206	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4928211	0.80[ASN][1000 genomes]
rs4928212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4928213	0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs56773086	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58846871	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67340958	0.80[ASN][1000 genomes]
rs6780095	0.83[EUR][1000 genomes]
rs72928493	0.96[EUR][1000 genomes]
rs72928498	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72930350	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72930363	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72930368	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72930370	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72932305	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72932315	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7613174	0.80[ASN][1000 genomes]
rs952924	0.80[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3755597	ST3GAL6	cis	lymphoblastoid	seeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99354400-99362000	Active TSS	Aorta	Aorta
2	chr3:99355200-99357600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:99355400-99357400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr3:99355600-99357400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:99355600-99357400	Active TSS	Right Ventricle	heart
6	chr3:99355600-99357600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr3:99355600-99357600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:99355600-99357800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
9	chr3:99355600-99357800	Active TSS	Colon Smooth Muscle	Colon
10	chr3:99355600-99360600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:99355800-99356800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:99355800-99356800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
13	chr3:99355800-99356800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:99355800-99357000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:99355800-99357200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:99355800-99357200	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr3:99355800-99357400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
18	chr3:99355800-99357400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
19	chr3:99355800-99357600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
20	chr3:99355800-99357600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
21	chr3:99355800-99357800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:99355800-99357800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
23	chr3:99355800-99358200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr3:99355800-99358600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr3:99355800-99358800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:99355800-99359400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:99355800-99360000	Active TSS	Right Atrium	heart
28	chr3:99356000-99356800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:99356000-99356800	Enhancers	Placenta Amnion	Placenta Amnion
30	chr3:99356000-99356800	Active TSS	Rectal Smooth Muscle	rectum
31	chr3:99356000-99357400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:99356000-99357400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
33	chr3:99356000-99357400	Active TSS	HMEC	breast
34	chr3:99356000-99357600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr3:99356000-99357600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:99356000-99357600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
37	chr3:99356000-99357600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
38	chr3:99356000-99357800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
39	chr3:99356000-99357800	Active TSS	Brain Cingulate Gyrus	brain
40	chr3:99356000-99357800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
41	chr3:99356000-99357800	Bivalent/Poised TSS	Fetal Kidney	kidney
42	chr3:99356000-99358000	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr3:99356000-99358000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:99356000-99358000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr3:99356000-99358000	Active TSS	Brain Anterior Caudate	brain
46	chr3:99356000-99358000	Active TSS	NHEK	skin
47	chr3:99356000-99358200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
48	chr3:99356000-99358400	Active TSS	HSMM	muscle
49	chr3:99356000-99359000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:99356000-99359000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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