Variant report

Variant	rs17162500
Chromosome Location	chr7:100451140-100451141
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	RUNX3	chr7:100450287-100451359	GM12878	blood:	n/a	n/a
2	SIN3AK20	chr7:100449333-100451194	MCF-7	breast:	n/a	n/a
3	CTCF	chr7:100451000-100451150	GM12871	blood:	n/a	chr7:100451028-100451041
4	MXI1	chr7:100449283-100451294	SK-N-SH	brain:	n/a	n/a
5	PAX5	chr7:100451029-100451491	GM12878	blood:	n/a	n/a
6	RAD21	chr7:100449109-100451174	SK-N-SH	brain:	n/a	chr7:100449819-100449838 chr7:100449823-100449837 chr7:100450317-100450331
7	MAX	chr7:100449643-100451341	GM12878	blood:	n/a	chr7:100450015-100450025
8	CTCF	chr7:100449189-100451309	SK-N-SH	brain:	n/a	chr7:100449823-100449836 chr7:100451028-100451041 chr7:100449821-100449839 chr7:100449816-100449837 chr7:100450107-100450120
9	PAX5	chr7:100451039-100451639	GM12878	blood:	n/a	n/a
10	PAX5	chr7:100451077-100451360	GM12892	blood:	n/a	n/a
11	MXI1	chr7:100449491-100451263	IMR90	lung:	n/a	n/a
12	STAT5A	chr7:100450754-100451229	GM12878	blood:	n/a	chr7:100451016-100451028
13	ELF1	chr7:100449537-100451170	MCF-7	breast:	n/a	chr7:100449831-100449844 chr7:100449835-100449844 chr7:100450105-100450117
14	PAX5	chr7:100451058-100451488	GM12878	blood:	n/a	n/a
15	PAX5	chr7:100451081-100451404	GM12891	blood:	n/a	n/a
16	MTA3	chr7:100450281-100451370	GM12878	blood:	n/a	n/a
17	MAX	chr7:100449600-100451228	NB4	blood:	n/a	chr7:100450015-100450025
18	ZNF384	chr7:100450930-100451477	GM12878	blood:	n/a	n/a
19	EP300	chr7:100450858-100451290	GM12878	blood:	n/a	chr7:100451031-100451047
20	ZNF384	chr7:100451058-100451368	K562	blood:	n/a	n/a
21	SPI1	chr7:100450628-100451341	HL-60	blood:	n/a	chr7:100450884-100450897
22	RUNX3	chr7:100450907-100451339	GM12878	blood:	n/a	n/a
23	EBF1	chr7:100450828-100451329	GM12878	blood:	n/a	n/a
24	SMC3	chr7:100449296-100451210	SK-N-SH	brain:	n/a	chr7:100451031-100451041 chr7:100450107-100450117 chr7:100449823-100449837
25	MYC	chr7:100449558-100451299	NB4	blood:	n/a	chr7:100450015-100450025
26	PAX5	chr7:100451140-100451389	GM12892	blood:	n/a	n/a
27	MXI1	chr7:100449627-100451340	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:100448636..100452358-chr7:100462094..100466806,6	K562	blood:
2	chr7:100424369..100426851-chr7:100449777..100451891,3	MCF-7	breast:
3	chr7:100422507..100426422-chr7:100448675..100454510,8	MCF-7	breast:
4	chr7:100450046..100452057-chr7:100463309..100465619,3	MCF-7	breast:
5	chr7:100025389..100027922-chr7:100449017..100452017,3	K562	blood:
6	chr7:100422826..100425783-chr7:100447402..100452140,5	K562	blood:
7	chr7:100301473..100305247-chr7:100448414..100451828,11	MCF-7	breast:
8	chr7:100448922..100451627-chr7:100483976..100487908,4	K562	blood:
9	chr7:100447367..100452420-chr7:100484839..100489079,9	MCF-7	breast:
10	chr7:100450060..100453457-chr7:100456779..100461941,7	MCF-7	breast:
11	chr7:100301718..100305707-chr7:100447040..100451705,6	K562	blood:
12	chr7:100450052..100452622-chr7:100454484..100455985,2	K562	blood:
13	chr7:100033058..100034813-chr7:100449764..100451334,2	K562	blood:
14	chr7:100423433..100426983-chr7:100448013..100452140,5	K562	blood:
15	chr7:100303112..100306288-chr7:100448604..100451276,4	MCF-7	breast:
16	chr7:100448750..100454655-chr7:100469427..100474218,6	MCF-7	breast:
17	chr7:100448977..100453392-chr7:100463620..100466806,5	K562	blood:
18	chr7:100449276..100451751-chr7:100451970..100455988,3	MCF-7	breast:
19	chr7:100448612..100451373-chr7:100457396..100459154,2	K562	blood:
20	chr7:100450381..100452181-chr7:100471838..100473668,2	K562	blood:

Variant related genes	Relation type
SLC12A9	TF binding region
ENSG00000236305	TF binding region
ENSG00000146828	Chromatin interaction
ENSG00000172336	Chromatin interaction
ENSG00000176125	Chromatin interaction
ENSG00000160813	Chromatin interaction
ENSG00000196411	Chromatin interaction
ENSG00000087077	Chromatin interaction
ENSG00000087087	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000240211	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17162522	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17880400	1.00[MEX][hapmap]
rs17883552	1.00[MEX][hapmap];0.82[YRI][hapmap]
rs55772336	1.00[AMR][1000 genomes]
rs57969015	1.00[AMR][1000 genomes]
rs60999863	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73714204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73714205	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73714206	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv1020837	chr7:100313122-100508635	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1832517	chr7:100355490-100749246	Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2758125	chr7:100355490-100749246	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	esv2759547	chr7:100355490-100749246	Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv464647	chr7:100374087-100497131	Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv607965	chr7:100374087-100497131	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv1032673	chr7:100382250-100606794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
9	nsv888797	chr7:100386900-100482026	Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
10	nsv888798	chr7:100406144-100472826	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv888799	chr7:100406144-100497131	Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
12	nsv888801	chr7:100416250-100497131	Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv464648	chr7:100422156-100518458	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
14	nsv607966	chr7:100422156-100518458	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
15	nsv831073	chr7:100425659-100544888	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100449200-100451400	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr7:100449400-100451200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:100449400-100451200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr7:100449400-100451200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr7:100449400-100451200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:100449400-100451200	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr7:100449400-100451200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr7:100449400-100451400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr7:100449400-100451400	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr7:100449600-100451200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr7:100449600-100451200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:100449600-100451200	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr7:100449600-100451200	Active TSS	HSMM	muscle
14	chr7:100449600-100451200	Active TSS	NHLF	lung
15	chr7:100449600-100451400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr7:100449600-100451400	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr7:100449600-100451400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:100449600-100451400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr7:100449600-100451400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr7:100449800-100451200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:100449800-100451200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:100449800-100451200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr7:100449800-100451200	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr7:100449800-100451200	Flanking Active TSS	Placenta	Placenta
25	chr7:100450000-100451400	Active TSS	Brain Hippocampus Middle	brain
26	chr7:100450200-100451200	Active TSS	Primary monocytes fromperipheralblood	blood
27	chr7:100450200-100451200	Active TSS	Right Ventricle	heart
28	chr7:100450200-100451200	Active TSS	NHDF-Ad	bronchial
29	chr7:100450400-100451200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr7:100450400-100451400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr7:100450600-100451200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr7:100450600-100451200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr7:100450600-100451200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:100450600-100451200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr7:100450600-100451200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr7:100450600-100451200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:100450600-100451200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr7:100450600-100451200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:100450600-100451200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr7:100450600-100451200	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr7:100450600-100451200	Flanking Active TSS	Fetal Muscle Trunk	muscle
42	chr7:100450600-100451200	Flanking Active TSS	Fetal Muscle Leg	muscle
43	chr7:100450600-100451200	Flanking Active TSS	Fetal Stomach	stomach
44	chr7:100450600-100451200	Flanking Active TSS	Fetal Thymus	thymus
45	chr7:100450600-100451200	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr7:100450600-100451200	Active TSS	Right Atrium	heart
47	chr7:100450600-100451200	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr7:100450600-100451200	Flanking Active TSS	Hela-S3	cervix
49	chr7:100450600-100451200	Flanking Active TSS	HUVEC	blood vessel
50	chr7:100450600-100451200	Flanking Active TSS	K562	blood

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