Variant report

Variant	rs11668998
Chromosome Location	chr19:51299342-51299343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:191)
CpG islands
(count:0)
Chromatin interactive
region (count:38)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:191 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:51294162-51303858	H1-hESC	embryonic stem cell:	n/a	n/a
2	BCL3	chr19:51296723-51300831	A549	lung:	n/a	chr19:51296878-51296891 chr19:51299623-51299631
3	POLR2A	chr19:51296363-51305119	HepG2	liver:	n/a	n/a
4	ATF2	chr19:51297404-51300281	GM12878	blood:	n/a	n/a
5	TCF12	chr19:51299065-51299352	GM12878	blood:	n/a	n/a
6	ATF2	chr19:51297146-51300313	GM12878	blood:	n/a	n/a
7	CHD2	chr19:51296875-51300537	K562	blood:	n/a	n/a
8	POLR2A	chr19:51296864-51303007	K562	blood:	n/a	n/a
9	NFIC	chr19:51297069-51299908	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:51292846-51302413	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr19:51296691-51300705	GM19099	blood:	n/a	n/a
12	POLR2A	chr19:51294069-51301549	U87	brain:	n/a	n/a
13	HEY1	chr19:51298114-51300748	K562	blood:	n/a	n/a
14	POLR2A	chr19:51294148-51303725	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr19:51296692-51299975	U87	brain:	n/a	n/a
16	CCNT2	chr19:51297579-51300481	K562	blood:	n/a	n/a
17	ATF1	chr19:51299082-51299680	K562	blood:	n/a	n/a
18	BCL3	chr19:51297840-51301578	K562	blood:	n/a	chr19:51299623-51299631
19	POLR2A	chr19:51295539-51303742	GM12891	blood:	n/a	n/a
20	ZNF263	chr19:51296948-51300470	HEK293-T-REx	kidney:	n/a	chr19:51298009-51298018
21	POLR2A	chr19:51294090-51301585	U87	brain:	n/a	n/a
22	POLR2A	chr19:51296564-51303843	HL-60	blood:	n/a	n/a
23	POLR2A	chr19:51293982-51303950	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:51296918-51304711	K562	blood:	n/a	n/a
25	SP1	chr19:51297419-51299459	A549	lung:	n/a	n/a
26	ZNF143	chr19:51299292-51299689	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr19:51296661-51302056	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:51292818-51303789	GM12891	blood:	n/a	n/a
29	MAX	chr19:51298851-51299356	K562	blood:	n/a	chr19:51299124-51299139 chr19:51299126-51299136 chr19:51299126-51299136
30	TCF12	chr19:51296667-51300851	A549	lung:	n/a	n/a
31	USF2	chr19:51297744-51300332	H1-hESC	embryonic stem cell:	n/a	chr19:51299616-51299632
32	PBX3	chr19:51296673-51300403	A549	lung:	n/a	n/a
33	GTF2F1	chr19:51297127-51299882	Hela-S3	cervix:	n/a	n/a
34	TEAD4	chr19:51297470-51300546	K562	blood:	n/a	n/a
35	POLR2A	chr19:51297423-51303234	GM12878	blood:	n/a	n/a
36	POLR2A	chr19:51297509-51299466	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr19:51297509-51300639	A549	lung:	n/a	n/a
38	POU2F2	chr19:51296090-51300827	GM12891	blood:	n/a	chr19:51297417-51297438 chr19:51299707-51299719
39	SIN3AK20	chr19:51297321-51300159	A549	lung:	n/a	n/a
40	PML	chr19:51296721-51300474	K562	blood:	n/a	n/a
41	POLR2A	chr19:51296584-51300695	GM12878	blood:	n/a	n/a
42	USF1	chr19:51297435-51299662	A549	lung:	n/a	chr19:51299616-51299632
43	POLR2A	chr19:51296672-51301538	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr19:51292766-51304914	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr19:51296785-51303813	GM18951	blood:	n/a	n/a
46	POU2F2	chr19:51296727-51300495	GM12891	blood:	n/a	chr19:51297417-51297438 chr19:51299707-51299719
47	MBD4	chr19:51297589-51300018	HepG2	liver:	n/a	n/a
48	KAP1	chr19:51298507-51299602	U2OS	brain:	n/a	n/a
49	ETS1	chr19:51297443-51300131	A549	lung:	n/a	chr19:51299364-51299371 chr19:51299593-51299606 chr19:51299707-51299720
50	HEY1	chr19:51298536-51300288	HepG2	liver:	n/a	n/a

No data

(count:38 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:51298931..51299437-chr6:7910784..7911331,2	HCT-116	colon:
2	chr19:51298041..51300435-chr19:51430470..51432377,2	K562	blood:
3	chr19:51287149..51288654-chr19:51298573..51300535,2	MCF-7	breast:
4	chr19:51297069..51301557-chr19:51353006..51355248,4	K562	blood:
5	chr19:51298091..51299895-chr19:51425770..51427626,2	MCF-7	breast:
6	chr19:51297217..51300572-chr19:51389305..51392408,3	MCF-7	breast:
7	chr19:51297754..51299382-chr19:51396945..51399003,2	K562	blood:
8	chr19:51296075..51301998-chr19:51356744..51362542,6	K562	blood:
9	chr19:51297209..51301271-chr19:51337976..51342137,10	K562	blood:
10	chr19:51298106..51301277-chr19:51425216..51427297,3	K562	blood:
11	chr19:51261730..51264544-chr19:51297937..51299631,2	K562	blood:
12	chr19:51036495..51041066-chr19:51297563..51301035,4	K562	blood:
13	chr19:51298113..51300783-chr19:51418876..51422103,3	MCF-7	breast:
14	chr19:51159348..51161376-chr19:51298352..51301122,3	K562	blood:
15	chr19:51289647..51292228-chr19:51297726..51299404,2	MCF-7	breast:
16	chr19:51210355..51211982-chr19:51296996..51299615,2	K562	blood:
17	chr19:51160675..51165510-chr19:51297124..51300859,8	K562	blood:
18	chr19:51297152..51303261-chr19:51371696..51377038,8	K562	blood:
19	chr19:51298843..51300590-chr19:51594747..51596538,2	K562	blood:
20	chr19:51226381..51234126-chr19:51290973..51302468,19	K562	blood:
21	chr19:51297173..51300001-chr19:51396139..51397785,2	MCF-7	breast:
22	chr19:51223222..51224739-chr19:51299062..51300801,2	K562	blood:
23	chr19:51202678..51205617-chr19:51298348..51299954,2	MCF-7	breast:
24	chr19:51298573..51300472-chr19:51395202..51396842,2	K562	blood:
25	chr19:51295821..51300740-chr19:51378160..51386074,8	K562	blood:
26	chr19:50834364..50836228-chr19:51297931..51300852,2	K562	blood:
27	chr19:51279277..51281371-chr19:51297725..51300722,2	K562	blood:
28	chr19:51200009..51202961-chr19:51298275..51301166,2	MCF-7	breast:
29	chr19:51297794..51299902-chr19:51431890..51433458,2	K562	blood:
30	chr19:51297375..51300335-chr19:51393395..51395432,2	MCF-7	breast:
31	chr19:51192657..51194532-chr19:51298388..51302132,3	K562	blood:
32	chr19:51227239..51229694-chr19:51298497..51300635,2	K562	blood:
33	chr19:51295821..51300740-chr19:51378160..51386074,7	K562	blood:
34	chr19:51058056..51060200-chr19:51298351..51300180,2	K562	blood:
35	chr19:51297907..51300191-chr19:51390481..51393453,2	K562	blood:
36	chr19:51206207..51210755-chr19:51296263..51301273,7	K562	blood:
37	chr19:51299041..51299831-chr8:104032716..104033360,2	HCT-116	colon:
38	chr19:51297246..51301277-chr19:51424078..51428279,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268375	TF binding region
ENSG00000239264	Chromatin interaction
ENSG00000228674	Chromatin interaction
ENSG00000197588	Chromatin interaction
ENSG00000155097	Chromatin interaction
ENSG00000105472	Chromatin interaction
ENSG00000161681	Chromatin interaction
ENSG00000167751	Chromatin interaction
ENSG00000235034	Chromatin interaction
ENSG00000142515	Chromatin interaction
ENSG00000174562	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10401588	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1043315	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10853825	0.86[CHD][hapmap];0.89[LWK][hapmap];0.91[YRI][hapmap]
rs11668685	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12052047	0.81[ASW][hapmap];0.86[CHD][hapmap]
rs12610777	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288417	0.81[ASW][hapmap];0.86[CHD][hapmap];0.86[LWK][hapmap];0.82[YRI][hapmap]
rs3212846	0.81[ASW][hapmap];0.86[CHD][hapmap]
rs3745526	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3745528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3865442	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3909863	0.86[CHD][hapmap]
rs4801853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802741	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802742	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs5517	0.83[CHD][hapmap]
rs5519	0.86[CHD][hapmap]
rs55735528	0.86[AMR][1000 genomes]
rs55929248	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv912288	chr19:51283791-51334355	Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv912289	chr19:51283791-51335943	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv912290	chr19:51283791-51344483	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11668998	MGC13170	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51287200-51301200	Weak transcription	Primary B cells from cord blood	blood
2	chr19:51287400-51300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr19:51291800-51303400	Weak transcription	Fetal Kidney	kidney
4	chr19:51293400-51300000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr19:51295600-51301000	Weak transcription	HepG2	liver
6	chr19:51296000-51300200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:51296000-51300400	Weak transcription	Fetal Lung	lung
8	chr19:51296400-51300600	Weak transcription	Brain Angular Gyrus	brain
9	chr19:51296600-51304200	Weak transcription	HSMM	muscle
10	chr19:51296800-51299800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr19:51297000-51300000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:51297000-51301000	Weak transcription	HSMMtube	muscle
13	chr19:51297000-51306200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr19:51297200-51299600	Weak transcription	Lung	lung
15	chr19:51297200-51299800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr19:51297200-51300000	Strong transcription	Right Atrium	heart
17	chr19:51297200-51300400	Weak transcription	Brain Anterior Caudate	brain
18	chr19:51297400-51299600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr19:51297400-51299600	Weak transcription	NHEK	skin
20	chr19:51297400-51300200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:51297400-51300200	Weak transcription	Brain Substantia Nigra	brain
22	chr19:51297400-51300400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr19:51297600-51300000	Weak transcription	Brain Hippocampus Middle	brain
24	chr19:51297600-51300400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr19:51297600-51301200	Weak transcription	NH-A	brain
26	chr19:51297600-51301200	Weak transcription	Osteobl	bone
27	chr19:51297600-51304200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr19:51297800-51299600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr19:51297800-51299800	Weak transcription	Placenta	Placenta
30	chr19:51297800-51300000	Weak transcription	Adipose Nuclei	Adipose
31	chr19:51297800-51300800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:51297800-51301000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr19:51297800-51305600	Weak transcription	Fetal Brain Male	brain
34	chr19:51297800-51306200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr19:51298000-51299400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr19:51298000-51300200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr19:51298000-51300400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:51298000-51300400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr19:51298000-51300400	Weak transcription	Colon Smooth Muscle	Colon
40	chr19:51298000-51303000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr19:51298000-51305400	Weak transcription	Fetal Heart	heart
42	chr19:51298200-51299800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr19:51298200-51299800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr19:51298200-51299800	Weak transcription	Hela-S3	cervix
45	chr19:51298200-51300200	Weak transcription	Fetal Intestine Large	intestine
46	chr19:51298200-51300400	Weak transcription	Left Ventricle	heart
47	chr19:51298200-51300600	Weak transcription	Rectal Smooth Muscle	rectum
48	chr19:51298200-51305400	Strong transcription	Fetal Intestine Small	intestine
49	chr19:51298200-51305400	Strong transcription	Fetal Stomach	stomach
50	chr19:51298200-51305800	Strong transcription	Brain Germinal Matrix	brain

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