Variant report

Variant	rs7246799
Chromosome Location	chr19:56160399-56160400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56110653..56113509-chr19:56160158..56165183,5	MCF-7	breast:
2	chr19:56158129..56161096-chr19:56185326..56187791,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171443	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000267523	Chromatin interaction
ENSG00000179943	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11545669	1.00[AFR][1000 genomes]
rs310439	1.00[AFR][1000 genomes]
rs310443	1.00[AFR][1000 genomes]
rs310470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310474	1.00[EUR][1000 genomes]
rs507498	0.83[EUR][1000 genomes]
rs520125	0.83[ASN][1000 genomes]
rs522669	0.83[ASN][1000 genomes]
rs553947	1.00[ASN][1000 genomes]
rs56038728	1.00[AFR][1000 genomes]
rs57063593	0.83[EUR][1000 genomes]
rs581023	0.84[EUR][1000 genomes]
rs600106	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs612211	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630491	1.00[AFR][1000 genomes]
rs636466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637788	0.89[EUR][1000 genomes]
rs644230	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs679577	0.83[EUR][1000 genomes]
rs680444	0.83[EUR][1000 genomes]
rs681433	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7251872	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs889091	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers 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	86 gene(s)	inside rSNPs	diseases
5	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
7	nsv912503	chr19:56149077-56162776	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
8	nsv912504	chr19:56149077-56170415	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer 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	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56158200-56160800	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr19:56158200-56161800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr19:56158400-56160600	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr19:56158400-56161000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr19:56158400-56161200	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr19:56158600-56160800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:56158600-56160800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr19:56158800-56160400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr19:56158800-56160400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr19:56158800-56160400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:56158800-56160400	Active TSS	HSMMtube	muscle
12	chr19:56159000-56160400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:56159000-56160400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:56159000-56160400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr19:56159000-56160400	Flanking Active TSS	HMEC	breast
16	chr19:56159000-56160600	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr19:56159000-56160600	Flanking Active TSS	Placenta	Placenta
18	chr19:56159000-56160800	Active TSS	Fetal Kidney	kidney
19	chr19:56159000-56161000	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr19:56159000-56161000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr19:56159200-56160400	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr19:56159200-56160600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:56159200-56160600	Active TSS	Colon Smooth Muscle	Colon
24	chr19:56159200-56160600	Active TSS	HepG2	liver
25	chr19:56159200-56160800	Active TSS	HSMM	muscle
26	chr19:56159400-56160400	Active TSS	Hela-S3	cervix
27	chr19:56159400-56160600	Active TSS	Fetal Brain Female	brain
28	chr19:56159400-56160600	Active TSS	NHLF	lung
29	chr19:56159600-56160600	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr19:56159800-56160400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:56159800-56160400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:56159800-56160400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:56159800-56160400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:56159800-56160400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr19:56159800-56160400	Flanking Active TSS	Fetal Muscle Leg	muscle
36	chr19:56159800-56160400	Flanking Active TSS	HUVEC	blood vessel
37	chr19:56159800-56160600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr19:56159800-56160600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr19:56159800-56160600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr19:56159800-56160600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:56159800-56160600	Flanking Active TSS	Colonic Mucosa	Colon
42	chr19:56159800-56160600	Flanking Active TSS	Fetal Thymus	thymus
43	chr19:56159800-56160600	Flanking Active TSS	Gastric	stomach
44	chr19:56159800-56160800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr19:56159800-56160800	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr19:56159800-56160800	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr19:56159800-56161000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr19:56159800-56161000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr19:56159800-56161000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr19:56159800-56161200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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