Variant report

Variant	rs58312319
Chromosome Location	chr7:7217785-7217786
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	SIN3AK20	chr7:7217643-7218317	MCF-7	breast:	n/a	n/a
2	FOSL2	chr7:7217684-7218225	MCF-7	breast:	n/a	chr7:7218040-7218049
3	GATA3	chr7:7217561-7218120	MCF-7	breast:	n/a	n/a
4	MYC	chr7:7217770-7218173	MCF10A-Er-Src	breast:	n/a	n/a
5	JUND	chr7:7217510-7218174	MCF-7	breast:	n/a	chr7:7218040-7218049
6	ZNF217	chr7:7217595-7218084	MCF-7	breast:	n/a	n/a
7	GATA2	chr7:7217628-7218017	SH-SY5Y	brain:	n/a	n/a
8	GATA3	chr7:7217558-7218223	T-47D	breast:	n/a	n/a
9	FOS	chr7:7217736-7219013	MCF10A-Er-Src	breast:	n/a	chr7:7218040-7218049
10	FOS	chr7:7217783-7218159	MCF10A-Er-Src	breast:	n/a	chr7:7218040-7218049
11	NR2F2	chr7:7217524-7218132	MCF-7	breast:	n/a	n/a
12	STAT3	chr7:7217647-7217920	MCF10A-Er-Src	breast:	n/a	n/a
13	SIN3AK20	chr7:7217472-7218303	MCF-7	breast:	n/a	n/a
14	CEBPB	chr7:7217691-7218227	MCF-7	breast:	n/a	n/a
15	NR2F2	chr7:7217583-7218129	MCF-7	breast:	n/a	n/a
16	FOSL2	chr7:7217657-7218174	MCF-7	breast:	n/a	chr7:7218040-7218049
17	TCF12	chr7:7217511-7218178	MCF-7	breast:	n/a	n/a
18	FOS	chr7:7217769-7218194	MCF10A-Er-Src	breast:	n/a	chr7:7218040-7218049
19	CEBPB	chr7:7217659-7218256	MCF-7	breast:	n/a	n/a
20	GATA3	chr7:7217260-7218428	MCF-7	breast:	n/a	chr7:7217349-7217359
21	FOXA1	chr7:7217762-7218084	T-47D	breast:	n/a	n/a
22	GATA3	chr7:7217640-7218134	MCF-7	breast:	n/a	n/a
23	TCF7L2	chr7:7217565-7218110	MCF-7	breast:	n/a	chr7:7217819-7217833
24	GATA3	chr7:7217446-7218336	MCF-7	breast:	n/a	n/a
25	FOS	chr7:7217742-7218278	MCF10A-Er-Src	breast:	n/a	chr7:7218040-7218049
26	GATA3	chr7:7217607-7218134	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:7213763..7219997-chr7:7220116..7223880,12	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RSPH10B2-2	chr7:7217583-7217955	NONHSAT119101

Variant related genes	Relation type
C1GALT1	TF binding region
ENSG00000106392	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10447684	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13238772	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17164011	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17249770	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17250084	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17309555	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2116533	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2116534	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2116535	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2163638	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2163639	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34386799	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34419200	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34491888	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34705126	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34971257	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4324853	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4428582	0.87[EUR][1000 genomes]
rs4582461	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58843310	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61465425	0.80[EUR][1000 genomes]
rs62449960	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62449964	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62449965	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62453487	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62453491	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62453504	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62453505	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62453506	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62453507	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62453510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62453511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62453512	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62453513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9648103	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv428160	chr7:6936949-7219553	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1020929	chr7:6954959-7232920	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats 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	39 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv508445	chr7:7190518-7261098	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
19	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
20	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58312319	C1GALT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7205800-7220800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr7:7205800-7220800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr7:7211200-7220400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr7:7212000-7220400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr7:7212800-7218800	Strong transcription	Primary B cells from cord blood	blood
6	chr7:7212800-7220800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr7:7213000-7220400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:7213000-7220400	Weak transcription	Dnd41	blood
9	chr7:7213400-7219800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:7213600-7220800	Enhancers	HMEC	breast
11	chr7:7215000-7217800	Enhancers	Fetal Intestine Large	intestine
12	chr7:7215200-7217800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr7:7215200-7217800	Enhancers	HSMM	muscle
14	chr7:7215200-7218800	Enhancers	Placenta Amnion	Placenta Amnion
15	chr7:7215400-7217800	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr7:7215400-7218200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:7215400-7218800	Enhancers	Hela-S3	cervix
18	chr7:7215400-7218800	Enhancers	Osteobl	bone
19	chr7:7215800-7218400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr7:7216000-7217800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr7:7216000-7218000	Enhancers	Fetal Intestine Small	intestine
22	chr7:7216000-7220800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr7:7216600-7218200	Enhancers	NHLF	lung
24	chr7:7216800-7217800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr7:7216800-7217800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr7:7216800-7217800	Enhancers	HUVEC	blood vessel
27	chr7:7216800-7218800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:7216800-7218800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:7216800-7218800	Enhancers	NHDF-Ad	bronchial
30	chr7:7216800-7219800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:7216800-7219800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:7216800-7220200	Enhancers	NHEK	skin
33	chr7:7216800-7220400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr7:7216800-7220800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr7:7216800-7220800	Weak transcription	Adipose Nuclei	Adipose
36	chr7:7216800-7221000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr7:7216800-7221200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr7:7217000-7219800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr7:7217000-7219800	Weak transcription	K562	blood
40	chr7:7217000-7220400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr7:7217000-7220400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr7:7217000-7220400	Weak transcription	HSMMtube	muscle
43	chr7:7217000-7220400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr7:7217000-7220600	Weak transcription	Primary T cells from cord blood	blood
45	chr7:7217000-7220800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr7:7217000-7220800	Weak transcription	Small Intestine	intestine
47	chr7:7217000-7221000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:7217000-7221000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr7:7217200-7218600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:7217200-7220400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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