Variant report

Variant	rs17252812
Chromosome Location	chr7:7298188-7298189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10487590	1.00[ASW][hapmap];0.81[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs12702597	0.84[AMR][1000 genomes]
rs13221206	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13225339	0.81[EUR][1000 genomes]
rs17166154	1.00[CHD][hapmap]
rs17251749	1.00[ASW][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs2116533	0.81[MEX][hapmap]
rs2116535	0.81[MEX][hapmap]
rs2163639	0.81[MEX][hapmap];1.00[YRI][hapmap]
rs35362940	0.82[AMR][1000 genomes]
rs4582461	0.81[MEX][hapmap];1.00[YRI][hapmap]
rs62450016	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62450018	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62450786	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015277	chr7:6705439-7303195	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1023133	chr7:6854098-7516700	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers 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	58 gene(s)	inside rSNPs	diseases
3	nsv869091	chr7:6927461-7567820	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
5	nsv464300	chr7:7040176-7368699	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv606033	chr7:7040176-7368699	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv1016369	chr7:7053923-7375567	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv1023788	chr7:7053923-7407783	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	nsv538720	chr7:7053923-7407783	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
10	nsv1032813	chr7:7053923-7497484	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv1030246	chr7:7053923-7569633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
12	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
13	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
14	nsv1032974	chr7:7145831-7393218	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
16	esv2758102	chr7:7209911-7493901	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
17	esv2759505	chr7:7209911-7493901	Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
18	nsv464301	chr7:7252775-7442169	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
19	nsv606035	chr7:7252775-7442169	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
20	nsv469770	chr7:7261414-7453821	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
21	nsv433018	chr7:7269171-7348778	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
22	nsv606036	chr7:7273559-7343909	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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
23	esv2756798	chr7:7280062-7441775	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
24	nsv8042	chr7:7291138-7328841	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	esv3475554	chr7:7291482-7325374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
26	esv3475552	chr7:7291507-7325362	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
27	esv3475555	chr7:7291507-7325362	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
28	nsv523128	chr7:7292458-7317960	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
29	nsv606037	chr7:7292458-7324800	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
30	nsv525648	chr7:7292892-7300923	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
31	nsv1016969	chr7:7294603-7317605	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
32	nsv1030528	chr7:7294603-7324800	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
33	esv2753039	chr7:7294800-7317600	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17252812	C1GALT1	Cis_1M	lymphoblastoid	RTeQTL
rs17252812	C1GALT1	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7257600-7298200	Weak transcription	Ovary	ovary
2	chr7:7257600-7299800	Weak transcription	Fetal Stomach	stomach
3	chr7:7261600-7299400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:7271400-7298200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:7273400-7311200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:7274600-7301600	Weak transcription	Brain Germinal Matrix	brain
7	chr7:7275600-7298200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:7275600-7305400	Weak transcription	Gastric	stomach
9	chr7:7276200-7298600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr7:7276800-7304000	Weak transcription	Fetal Brain Male	brain
11	chr7:7277200-7306200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:7278400-7299600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:7279200-7298600	Weak transcription	Thymus	Thymus
14	chr7:7279200-7309800	Weak transcription	Brain Anterior Caudate	brain
15	chr7:7279800-7300000	Weak transcription	Fetal Brain Female	brain
16	chr7:7279800-7301000	Weak transcription	A549	lung
17	chr7:7279800-7304600	Weak transcription	NHDF-Ad	bronchial
18	chr7:7280000-7299800	Weak transcription	Placenta	Placenta
19	chr7:7280000-7300200	Weak transcription	NH-A	brain
20	chr7:7280000-7300400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr7:7280000-7302800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr7:7283400-7299800	Weak transcription	K562	blood
23	chr7:7283800-7300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr7:7284200-7298600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr7:7284400-7299600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr7:7285000-7300400	Weak transcription	Esophagus	oesophagus
27	chr7:7285000-7310600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:7285400-7302800	Weak transcription	HSMMtube	muscle
29	chr7:7287400-7301000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr7:7289600-7300200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr7:7291200-7298600	Strong transcription	HSMM	muscle
32	chr7:7291400-7298400	Weak transcription	Adipose Nuclei	Adipose
33	chr7:7291600-7299800	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr7:7291800-7298600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr7:7291800-7300200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr7:7291800-7304400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:7292200-7299600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr7:7294800-7298200	Weak transcription	HepG2	liver
39	chr7:7294800-7299600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr7:7295400-7298600	Enhancers	Duodenum Mucosa	Duodenum
41	chr7:7295400-7299200	Weak transcription	Stomach Mucosa	stomach
42	chr7:7295600-7300600	Weak transcription	Fetal Intestine Large	intestine
43	chr7:7296200-7298200	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr7:7296200-7298200	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr7:7296200-7299800	Strong transcription	Osteobl	bone
46	chr7:7296400-7298400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr7:7296600-7298200	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr7:7296600-7298200	Enhancers	Small Intestine	intestine
49	chr7:7296600-7298400	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr7:7296600-7298400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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