Variant report

Variant	rs231239
Chromosome Location	chr19:36248262-36248263
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	RCOR1	chr19:36248240-36248303	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:36247961-36249593	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr19:36248252-36248686	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr19:36247523-36249660	U87	brain:	n/a	n/a
5	SP1	chr19:36248145-36249680	HCT-116	colon:	n/a	chr19:36249017-36249029 chr19:36249018-36249028 chr19:36249014-36249028 chr19:36249456-36249468 chr19:36248961-36248982 chr19:36249019-36249028 chr19:36249018-36249027 chr19:36249017-36249029 chr19:36249017-36249028 chr19:36249019-36249028 chr19:36249018-36249028
6	POLR2A	chr19:36247429-36249863	PANC-1	pancreas:	n/a	n/a
7	TCF12	chr19:36247866-36249803	SK-N-SH	brain:	n/a	chr19:36248579-36248589
8	POLR2A	chr19:36247887-36249617	PFSK-1	brain:	n/a	n/a
9	EP300	chr19:36247984-36249247	SK-N-SH	brain:	n/a	n/a
10	REST	chr19:36248257-36248692	SK-N-SH	brain:	n/a	chr19:36248543-36248556
11	POLR2A	chr19:36247565-36249515	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr19:36243424-36249712	IMR90	lung:	n/a	n/a
13	MAZ	chr19:36248207-36249541	Hela-S3	cervix:	n/a	n/a
14	SIX5	chr19:36247941-36249863	A549	lung:	n/a	chr19:36249248-36249257 chr19:36249246-36249255 chr19:36249244-36249258
15	CREB1	chr19:36248248-36249659	A549	lung:	n/a	n/a
16	POLR2A	chr19:36248182-36249565	PBDE	blood:	n/a	n/a
17	MAX	chr19:36248141-36249747	A549	lung:	n/a	n/a
18	POLR2A	chr19:36247962-36249523	HCT-116	colon:	n/a	n/a
19	TCF12	chr19:36248049-36248822	SK-N-SH	brain:	n/a	chr19:36248579-36248589
20	POLR2A	chr19:36248177-36249491	HepG2	liver:	n/a	n/a
21	POLR2A	chr19:36248158-36249560	K562	blood:	n/a	n/a
22	POLR2A	chr19:36248223-36249503	H1-hESC	embryonic stem cell:	n/a	n/a
23	PBX3	chr19:36247547-36249734	A549	lung:	n/a	chr19:36248844-36248864 chr19:36248627-36248636
24	NFIC	chr19:36248185-36248487	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:36247499-36249815	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr19:36248121-36249439	K562	blood:	n/a	n/a
27	TAF1	chr19:36248167-36249579	SK-N-SH	brain:	n/a	n/a
28	SP1	chr19:36248255-36249230	K562	blood:	n/a	chr19:36249017-36249029 chr19:36249018-36249028 chr19:36249014-36249028 chr19:36248961-36248982 chr19:36249019-36249028 chr19:36249018-36249027 chr19:36249017-36249029 chr19:36249017-36249028 chr19:36249019-36249028 chr19:36249018-36249028
29	POLR2A	chr19:36248184-36249513	Raji	blood:	n/a	n/a
30	POLR2A	chr19:36247552-36249488	HCT-116	colon:	n/a	n/a
31	NFIC	chr19:36247965-36248887	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr19:36247869-36249639	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr19:36247442-36249646	HUVEC	blood vessel:	n/a	n/a
34	ETS1	chr19:36247902-36249774	A549	lung:	n/a	chr19:36248677-36248688 chr19:36249244-36249257 chr19:36249245-36249258 chr19:36249092-36249102 chr19:36249479-36249492 chr19:36249091-36249102 chr19:36249480-36249493
35	POLR2A	chr19:36248246-36248456	HepG2	liver:	n/a	n/a
36	CTCF	chr19:36248200-36248350	BE2_C	brain:	n/a	n/a
37	POLR2A	chr19:36247073-36249660	U87	brain:	n/a	n/a
38	MTA3	chr19:36247903-36248309	GM12878	blood:	n/a	n/a
39	SIN3A	chr19:36247680-36249608	H1-hESC	embryonic stem cell:	n/a	chr19:36249080-36249091
40	FOSL1	chr19:36248192-36248629	K562	blood:	n/a	n/a
41	PBX3	chr19:36248018-36249425	SK-N-SH	brain:	n/a	chr19:36248844-36248864 chr19:36248627-36248636
42	POLR2A	chr19:36248076-36249553	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr19:36248078-36249535	K562	blood:	n/a	n/a
44	POLR2A	chr19:36248235-36248340	Gliobla	brain:	n/a	n/a
45	TBL1XR1	chr19:36248227-36248296	GM12878	blood:	n/a	n/a
46	BCL3	chr19:36247910-36249677	A549	lung:	n/a	chr19:36249091-36249100
47	POLR2A	chr19:36247659-36249513	Hela-S3	cervix:	n/a	n/a
48	MAZ	chr19:36245970-36249729	IMR90	lung:	n/a	chr19:36246654-36246663
49	MAX	chr19:36247955-36250006	A549	lung:	n/a	n/a
50	POLR2A	chr19:36248252-36249437	GM18951	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36247404..36252021-chr19:36265348..36272678,7	MCF-7	breast:
2	chr19:36206099..36210841-chr19:36246614..36251827,8	MCF-7	breast:
3	chr19:36245255..36250047-chr19:36263979..36267864,8	K562	blood:
4	chr19:36238866..36244880-chr19:36246037..36252437,21	MCF-7	breast:
5	chr19:36247959..36249985-chr19:36390079..36391606,2	MCF-7	breast:
6	chr19:36247584..36253409-chr19:36264102..36268750,7	K562	blood:

Variant related genes	Relation type
HSPB6	TF binding region
ENSG00000267439	TF binding region
C19orf55	TF binding region
ENSG00000267439	Chromatin interaction
ENSG00000004777	Chromatin interaction
ENSG00000267796	Chromatin interaction
ENSG00000272333	Chromatin interaction
ENSG00000167604	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1262746	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1262750	1.00[AMR][1000 genomes]
rs1262751	1.00[AMR][1000 genomes]
rs1268319	0.88[AFR][1000 genomes]
rs179569	1.00[AMR][1000 genomes]
rs231215	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs231219	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs231220	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs231224	1.00[AMR][1000 genomes]
rs231240	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs231587	1.00[AMR][1000 genomes]
rs231595	1.00[AMR][1000 genomes]
rs2428145	1.00[AMR][1000 genomes]
rs2520310	1.00[AMR][1000 genomes]
rs73931233	1.00[AMR][1000 genomes]
rs807490	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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription 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	61 gene(s)	inside rSNPs	diseases
8	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
9	nsv543996	chr19:36210269-36265431	Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS 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 lncRNA	45 gene(s)	inside rSNPs	diseases
14	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
15	nsv911636	chr19:36240960-36290977	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 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	chr19:36245800-36248400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:36246000-36248400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
3	chr19:36246000-36248600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr19:36246000-36248600	Enhancers	Spleen	Spleen
5	chr19:36246000-36248800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr19:36246000-36248800	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr19:36246000-36248800	Flanking Active TSS	Fetal Muscle Trunk	muscle
8	chr19:36246000-36249800	Active TSS	H9 Cell Line	embryonic stem cell
9	chr19:36246200-36248400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:36246200-36248400	Flanking Active TSS	Left Ventricle	heart
11	chr19:36246200-36248600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr19:36246200-36248600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr19:36246200-36248800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:36246200-36248800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr19:36246200-36249400	Active TSS	Aorta	Aorta
16	chr19:36246200-36250000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr19:36246400-36248800	Flanking Active TSS	Fetal Muscle Leg	muscle
18	chr19:36246400-36249800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:36246400-36249800	Active TSS	Rectal Smooth Muscle	rectum
20	chr19:36246400-36250000	Active TSS	Psoas Muscle	Psoas
21	chr19:36246400-36250200	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr19:36246800-36248400	Enhancers	Liver	Liver
23	chr19:36246800-36248400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
24	chr19:36246800-36248600	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr19:36246800-36248800	Flanking Active TSS	Placenta	Placenta
26	chr19:36246800-36248800	Flanking Active TSS	NH-A	brain
27	chr19:36247000-36248400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr19:36247000-36248400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr19:36247000-36248400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:36247000-36248400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:36247000-36248600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:36247000-36248600	Enhancers	Fetal Brain Male	brain
33	chr19:36247000-36248800	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr19:36247200-36248400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:36247200-36249600	Active TSS	Ovary	ovary
36	chr19:36247200-36250000	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr19:36247400-36248600	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr19:36247400-36248600	Flanking Active TSS	Fetal Brain Female	brain
39	chr19:36247400-36248800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr19:36247400-36249800	Active TSS	Fetal Kidney	kidney
41	chr19:36247600-36248400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr19:36247600-36248400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:36247600-36248400	Flanking Bivalent TSS/Enh	Thymus	Thymus
44	chr19:36247600-36248400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
45	chr19:36247600-36248400	Flanking Active TSS	NHLF	lung
46	chr19:36247600-36248600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:36247600-36248600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr19:36247600-36248600	Flanking Active TSS	Brain Anterior Caudate	brain
49	chr19:36247600-36248600	Flanking Active TSS	Brain Cingulate Gyrus	brain
50	chr19:36247600-36248600	Flanking Active TSS	Brain Germinal Matrix	brain

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