Variant report

Variant	rs56250754
Chromosome Location	chr7:7962993-7962994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:7961731..7965503-chr7:8006784..8010279,5	MCF-7	breast:
2	chr7:7960775..7968037-chr7:8006243..8012214,13	MCF-7	breast:
3	chr7:7958223..7960322-chr7:7962105..7964489,3	MCF-7	breast:
4	chr18:3245457..3248097-chr7:7961361..7963995,2	MCF-7	breast:
5	chr7:7949577..7953346-chr7:7959266..7963720,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272688	Chromatin interaction
ENSG00000233108	Chromatin interaction
ENSG00000101608	Chromatin interaction
ENSG00000214998	Chromatin interaction
ENSG00000106415	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10237854	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10263240	0.96[ASN][1000 genomes]
rs10282585	0.91[ASN][1000 genomes]
rs2041565	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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	59 gene(s)	inside rSNPs	diseases
3	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1030180	chr7:7860424-8059221	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv464304	chr7:7913819-7970560	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv606046	chr7:7913819-7970560	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3346837	chr7:7915187-8068557	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1020161	chr7:7929384-8047553	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv525502	chr7:7938596-7996590	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv606048	chr7:7938596-7996590	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv606049	chr7:7949059-7967424	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7942600-7963600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:7953600-7963200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:7957600-7964600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr7:7957800-7964200	Enhancers	Primary B cells from peripheral blood	blood
5	chr7:7958000-7964600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr7:7958400-7964600	Enhancers	Primary B cells from cord blood	blood
7	chr7:7960000-7964000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:7960400-7963600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr7:7960600-7963200	Weak transcription	Primary T cells from cord blood	blood
10	chr7:7960800-7964000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr7:7960800-7964200	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr7:7961000-7963200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr7:7961000-7963200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr7:7961000-7963200	Enhancers	GM12878-XiMat	blood
15	chr7:7961000-7963400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr7:7961400-7964400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr7:7961400-7964600	Enhancers	Stomach Mucosa	stomach
18	chr7:7961600-7963000	Enhancers	Fetal Intestine Large	intestine
19	chr7:7961600-7963200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:7961600-7963200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr7:7961600-7964000	Enhancers	Brain Germinal Matrix	brain
22	chr7:7961600-7964400	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr7:7961600-7964600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr7:7961600-7964600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:7961800-7963000	Enhancers	Duodenum Mucosa	Duodenum
26	chr7:7961800-7963200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr7:7961800-7963600	Enhancers	Brain Cingulate Gyrus	brain
28	chr7:7961800-7975800	Weak transcription	Fetal Stomach	stomach
29	chr7:7962000-7964600	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr7:7962200-7963000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr7:7962200-7963200	Weak transcription	Thymus	Thymus
32	chr7:7962200-7963600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr7:7962200-7964000	Weak transcription	Gastric	stomach
34	chr7:7962400-7963000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:7962400-7963400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr7:7962400-7964200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:7962600-7963000	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr7:7962600-7964200	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr7:7962600-7964600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr7:7962800-7963000	Enhancers	Brain Hippocampus Middle	brain
41	chr7:7962800-7963400	Enhancers	Brain Anterior Caudate	brain
42	chr7:7962800-7963800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr7:7962800-7963800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr7:7962800-7963800	Weak transcription	HepG2	liver
45	chr7:7962800-7964600	Enhancers	Dnd41	blood

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