Variant report

Variant	rs7249940
Chromosome Location	chr19:19518010-19518011
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	CTCF	chr19:19517900-19518050	GM12872	blood:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
2	SIN3AK20	chr19:19515685-19518134	MCF-7	breast:	n/a	n/a
3	CTCF	chr19:19517880-19518030	HCPEpiC	choroid plexus:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
4	CTCF	chr19:19517858-19518031	GM10248	blood:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
5	MAX	chr19:19517816-19518318	K562	blood:	n/a	n/a
6	RFX5	chr19:19517387-19518086	Hela-S3	cervix:	n/a	n/a
7	JUND	chr19:19517657-19518188	K562	blood:	n/a	chr19:19517812-19517822 chr19:19517812-19517822 chr19:19517812-19517822 chr19:19517809-19517820
8	CTCF	chr19:19517880-19518030	HMF	breast:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
9	RAD21	chr19:19517675-19518144	HepG2	liver:	n/a	chr19:19517920-19517939 chr19:19517930-19517944 chr19:19518047-19518059
10	CTCF	chr19:19517839-19518032	NHEK	skin:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
11	CTCF	chr19:19517860-19518010	HMEC	breast:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
12	CTCF	chr19:19517823-19518058	MCF-7	breast:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
13	CTCF	chr19:19517860-19518010	GM12865	blood:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
14	RAD21	chr19:19517819-19518013	K562	blood:	n/a	chr19:19517920-19517939 chr19:19517930-19517944
15	POLR2A	chr19:19517348-19518616	GM12892	blood:	n/a	n/a
16	RAD21	chr19:19517652-19518106	Hela-S3	cervix:	n/a	chr19:19517920-19517939 chr19:19517930-19517944 chr19:19518047-19518059
17	CTCF	chr19:19517860-19518010	GM12878	blood:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
18	CTCF	chr19:19517839-19518040	Gliobla	brain:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
19	CTCF	chr19:19517880-19518030	SK-N-SH_RA	brain:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
20	CTCF	chr19:19517842-19518025	HepG2	liver:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
21	CTCF	chr19:19517860-19518010	HCPEpiC	choroid plexus:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
22	CTCF	chr19:19517814-19518069	MCF-7	breast:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
23	POLR2A	chr19:19515810-19518478	H1-hESC	embryonic stem cell:	n/a	n/a
24	MXI1	chr19:19515634-19518501	SK-N-SH	brain:	n/a	chr19:19517040-19517049
25	CTCF	chr19:19517827-19518038	GM10266	blood:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
26	MXI1	chr19:19515533-19518803	IMR90	lung:	n/a	chr19:19517040-19517049
27	TCF7L2	chr19:19517410-19518383	Hela-S3	cervix:	n/a	chr19:19517813-19517822 chr19:19517799-19517808 chr19:19517800-19517809 chr19:19517796-19517812 chr19:19517796-19517812
28	FOS	chr19:19517583-19518017	MCF10A-Er-Src	breast:	n/a	chr19:19517812-19517822 chr19:19517811-19517822 chr19:19517812-19517822 chr19:19517812-19517822 chr19:19517809-19517820
29	CTCF	chr19:19517900-19518050	GM12864	blood:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
30	RAD21	chr19:19517713-19518116	GM12878	blood:	n/a	chr19:19517920-19517939 chr19:19517930-19517944 chr19:19518047-19518059
31	CTCF	chr19:19517861-19518032	GM12891	blood:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
32	BCLAF1	chr19:19517251-19518163	GM12878	blood:	n/a	chr19:19517670-19517679
33	CTCF	chr19:19517833-19518047	MCF-7	breast:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
34	CTCF	chr19:19517832-19518056	LNCaP	prostate:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
35	CTCF	chr19:19517860-19518010	MCF-7	breast:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
36	CTCF	chr19:19517815-19518051	Hela-S3	cervix:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
37	CTCF	chr19:19517858-19518021	Kidney_OC	kidney:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
38	CTCF	chr19:19517900-19518050	HAc	cerebellar:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
39	CTCF	chr19:19517860-19518010	GM12873	blood:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
40	FOXM1	chr19:19517210-19518222	GM12878	blood:	n/a	n/a
41	CTCF	chr19:19517880-19518030	GM12873	blood:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
42	RAD21	chr19:19517835-19518065	GM12878	blood:	n/a	chr19:19517920-19517939 chr19:19517930-19517944 chr19:19518047-19518059
43	CTCF	chr19:19517855-19518022	GM13977	blood:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
44	CTCF	chr19:19517920-19518070	RPTEC	kidney:	n/a	chr19:19517922-19517940
45	CTCF	chr19:19517860-19518010	HPAF	blood vessel:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
46	CTCF	chr19:19517855-19518067	A549	lung:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
47	CTCF	chr19:19517762-19518095	IMR90	lung:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
48	MAZ	chr19:19515334-19518804	IMR90	lung:	n/a	chr19:19517185-19517192 chr19:19517317-19517326 chr19:19517183-19517194 chr19:19517184-19517193 chr19:19517184-19517194 chr19:19517168-19517178 chr19:19516393-19516403 chr19:19517041-19517050 chr19:19517043-19517052 chr19:19517042-19517049 chr19:19517186-19517195
49	CTCF	chr19:19517880-19518030	HMEC	breast:	n/a	chr19:19517922-19517940 chr19:19517917-19517938
50	ZNF143	chr19:19517783-19518061	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19516568..19518207-chr19:19573514..19577628,3	MCF-7	breast:
2	chr19:19517676..19523653-chr19:19565926..19570851,6	K562	blood:
3	chr19:19515140..19518800-chr19:19574675..19578008,3	K562	blood:
4	chr19:19492268..19501550-chr19:19512499..19523684,29	K562	blood:
5	chr13:93606573..93607451-chr19:19517462..19518161,2	MCF-7	breast:
6	chr19:19517676..19519463-chr19:19566372..19569188,2	K562	blood:
7	chr19:19517059..19519979-chr19:19556271..19558619,2	MCF-7	breast:
8	chr19:19477369..19478572-chr19:19517483..19518545,4	MCF-7	breast:
9	chr19:19491673..19504307-chr19:19513999..19523684,33	K562	blood:
10	chr19:19477386..19478234-chr19:19517375..19518109,3	MCF-7	breast:
11	chr19:19516170..19518046-chr20:30944497..30946734,2	K562	blood:
12	chr19:19517137..19518642-chr19:19558154..19560322,2	K562	blood:
13	chr19:19428553..19432587-chr19:19515649..19520173,6	K562	blood:
14	chr19:19514824..19526614-chr19:19535593..19543548,15	K562	blood:
15	chr19:19494732..19500297-chr19:19512585..19520288,14	MCF-7	breast:
16	chr19:19476063..19479194-chr19:19516845..19521061,4	K562	blood:
17	chr19:19454032..19456725-chr19:19515938..19518682,3	K562	blood:
18	chr19:19514840..19518062-chr19:19543803..19546421,4	K562	blood:
19	chr19:19477732..19478297-chr19:19517505..19518349,2	K562	blood:
20	chr19:19494550..19497983-chr19:19513188..19518336,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267234	TF binding region
ENSG00000105705	Chromatin interaction
ENSG00000207821	Chromatin interaction
ENSG00000171456	Chromatin interaction
ENSG00000129933	Chromatin interaction
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10402799	1.00[AMR][1000 genomes]
rs10403737	0.89[AFR][1000 genomes]
rs10408216	1.00[AMR][1000 genomes]
rs10413309	1.00[AMR][1000 genomes]
rs10413582	0.89[AFR][1000 genomes]
rs10417312	0.89[AMR][1000 genomes]
rs10417715	1.00[AMR][1000 genomes]
rs10422522	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423535	0.80[AFR][1000 genomes]
rs10423747	1.00[AMR][1000 genomes]
rs10425574	0.85[AFR][1000 genomes]
rs16996042	1.00[AMR][1000 genomes]
rs2106699	1.00[AMR][1000 genomes]
rs2315280	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56304704	1.00[AMR][1000 genomes]
rs56317107	1.00[AMR][1000 genomes]
rs60860168	1.00[AMR][1000 genomes]
rs7248765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922864	1.00[AMR][1000 genomes]
rs73922870	1.00[AMR][1000 genomes]
rs8110508	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9304961	0.89[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	esv3360569	chr19:19515477-19518325	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	esv3411112	chr19:19515802-19518225	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19515600-19518200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:19515800-19518200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr19:19515800-19518200	Active TSS	Ovary	ovary
4	chr19:19515800-19518200	Active TSS	Psoas Muscle	Psoas
5	chr19:19515800-19518800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:19516000-19518200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:19516000-19518200	Active TSS	Small Intestine	intestine
8	chr19:19516200-19518200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:19516200-19518400	Active TSS	HSMMtube	muscle
10	chr19:19516400-19518200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:19516400-19518200	Active TSS	Pancreas	Pancrea
12	chr19:19517400-19518200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:19517400-19518200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:19517400-19518200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr19:19517400-19518200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:19517400-19518200	Flanking Active TSS	Fetal Thymus	thymus
17	chr19:19517400-19518400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr19:19517400-19518400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr19:19517400-19518400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr19:19517400-19518400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:19517400-19518400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
22	chr19:19517400-19518400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr19:19517400-19518400	Flanking Active TSS	Brain Angular Gyrus	brain
24	chr19:19517400-19518400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
25	chr19:19517400-19518400	Flanking Active TSS	Fetal Muscle Trunk	muscle
26	chr19:19517400-19518400	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr19:19517400-19518400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr19:19517400-19518400	Flanking Active TSS	Thymus	Thymus
29	chr19:19517400-19518400	Flanking Active TSS	Dnd41	blood
30	chr19:19517400-19518400	Flanking Active TSS	HUVEC	blood vessel
31	chr19:19517400-19518600	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr19:19517400-19518600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr19:19517400-19518600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr19:19517400-19518600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr19:19517400-19518600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:19517400-19518600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr19:19517400-19518600	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr19:19517400-19518600	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr19:19517400-19518600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr19:19517400-19518600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr19:19517400-19518800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr19:19517400-19518800	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr19:19517400-19518800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr19:19517400-19518800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:19517400-19518800	Transcr. at gene 5' and 3'	K562	blood
46	chr19:19517400-19518800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr19:19517600-19518200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:19517600-19518200	Flanking Active TSS	Fetal Stomach	stomach
49	chr19:19517600-19518200	Flanking Active TSS	Stomach Mucosa	stomach
50	chr19:19517600-19518400	Flanking Active TSS	Primary T cells from cord blood	blood

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