Variant report

Variant	rs28588056
Chromosome Location	chr7:7219023-7219024
allele	C/T
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	FOS	chr7:7218521-7219164	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:7203286..7204986-chr7:7218086..7220030,2	K562	blood:
2	chr7:7152128..7153936-chr7:7218003..7219590,2	MCF-7	breast:
3	chr7:7213763..7219997-chr7:7220116..7223880,12	MCF-7	breast:

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

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10226438	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10240750	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10246194	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10246299	1.00[EUR][1000 genomes]
rs10246843	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10251676	1.00[EUR][1000 genomes]
rs10255843	1.00[EUR][1000 genomes]
rs10260209	1.00[EUR][1000 genomes]
rs10267375	1.00[EUR][1000 genomes]
rs10276239	1.00[EUR][1000 genomes]
rs11976941	1.00[EUR][1000 genomes]
rs11980424	1.00[EUR][1000 genomes]
rs11982566	1.00[EUR][1000 genomes]
rs13437710	1.00[EUR][1000 genomes]
rs13437711	1.00[EUR][1000 genomes]
rs1368052	1.00[EUR][1000 genomes]
rs2190934	1.00[EUR][1000 genomes]
rs28410769	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28421078	1.00[EUR][1000 genomes]
rs28872550	1.00[EUR][1000 genomes]
rs59821522	1.00[EUR][1000 genomes]
rs6975760	1.00[AMR][1000 genomes]
rs73335341	1.00[EUR][1000 genomes]
rs73337351	1.00[EUR][1000 genomes]
rs73674616	1.00[EUR][1000 genomes]
rs73674617	1.00[EUR][1000 genomes]
rs73674623	1.00[EUR][1000 genomes]
rs73674624	1.00[EUR][1000 genomes]
rs73674625	1.00[EUR][1000 genomes]
rs73674631	1.00[EUR][1000 genomes]
rs73674632	1.00[EUR][1000 genomes]
rs73674633	1.00[EUR][1000 genomes]
rs7784313	1.00[EUR][1000 genomes]
rs7788265	1.00[EUR][1000 genomes]
rs7790391	1.00[EUR][1000 genomes]
rs7804767	1.00[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

No data

Chromatin state (count:73 , 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	chr7:7212800-7220800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr7:7213000-7220400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:7213000-7220400	Weak transcription	Dnd41	blood
8	chr7:7213400-7219800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:7213600-7220800	Enhancers	HMEC	breast
10	chr7:7216000-7220800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr7:7216800-7219800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:7216800-7219800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:7216800-7220200	Enhancers	NHEK	skin
14	chr7:7216800-7220400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr7:7216800-7220800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:7216800-7220800	Weak transcription	Adipose Nuclei	Adipose
17	chr7:7216800-7221000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:7216800-7221200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:7217000-7219800	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr7:7217000-7219800	Weak transcription	K562	blood
21	chr7:7217000-7220400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr7:7217000-7220400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr7:7217000-7220400	Weak transcription	HSMMtube	muscle
24	chr7:7217000-7220400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr7:7217000-7220600	Weak transcription	Primary T cells from cord blood	blood
26	chr7:7217000-7220800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr7:7217000-7220800	Weak transcription	Small Intestine	intestine
28	chr7:7217000-7221000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:7217000-7221000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr7:7217200-7220400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr7:7217200-7220800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:7217200-7220800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:7217200-7220800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr7:7217200-7221200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr7:7217400-7220200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr7:7217400-7220400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr7:7217400-7220600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:7217400-7220800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr7:7217400-7220800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr7:7217400-7220800	Weak transcription	Fetal Kidney	kidney
41	chr7:7217600-7220400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr7:7217600-7220800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr7:7217600-7220800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr7:7217600-7220800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr7:7217600-7220800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr7:7217600-7220800	Weak transcription	Stomach Mucosa	stomach
47	chr7:7217600-7220800	Enhancers	HepG2	liver
48	chr7:7217600-7221000	Weak transcription	NH-A	brain
49	chr7:7217800-7220400	Weak transcription	Fetal Intestine Large	intestine
50	chr7:7217800-7220600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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