Variant report

Variant	rs16996127
Chromosome Location	chr19:19627310-19627311
allele	G/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	TAF1	chr19:19626719-19627446	PFSK-1	brain:	n/a	n/a
2	JUND	chr19:19626406-19627464	K562	blood:	n/a	chr19:19626492-19626501 chr19:19626491-19626502
3	POLR2A	chr19:19626458-19627436	K562	blood:	n/a	n/a
4	YY1	chr19:19626349-19627656	H1-hESC	embryonic stem cell:	n/a	chr19:19627191-19627200 chr19:19627043-19627055
5	MAX	chr19:19626465-19627353	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr19:19626559-19627404	ProgFib	skin:	n/a	n/a
7	RELA	chr19:19626729-19627422	GM19193	blood:	n/a	n/a
8	YY1	chr19:19626481-19627664	GM12878	blood:	n/a	chr19:19627191-19627200 chr19:19627043-19627055
9	MYC	chr19:19626566-19627585	NB4	blood:	n/a	chr19:19627553-19627563
10	POLR2A	chr19:19626733-19627326	HEK293	kidney:	n/a	n/a
11	POLR2A	chr19:19626458-19627312	GM12892	blood:	n/a	n/a
12	POLR2A	chr19:19626408-19627482	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr19:19626738-19627317	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:19626696-19627326	H1-hESC	embryonic stem cell:	n/a	n/a
15	TBP	chr19:19626660-19627425	GM12878	blood:	n/a	n/a
16	IRF1	chr19:19626759-19627443	K562	blood:	n/a	chr19:19627244-19627258 chr19:19627190-19627204
17	MAZ	chr19:19626482-19627477	GM12878	blood:	n/a	n/a
18	ELK4	chr19:19626444-19627311	Hela-S3	cervix:	n/a	chr19:19627022-19627033 chr19:19627007-19627018
19	ELF1	chr19:19626561-19627318	SK-N-SH	brain:	n/a	chr19:19627019-19627032 chr19:19627249-19627261
20	POLR2A	chr19:19626400-19627444	HCT-116	colon:	n/a	n/a
21	TAF1	chr19:19626716-19627437	SK-N-SH	brain:	n/a	n/a
22	GABPA	chr19:19626433-19627384	K562	blood:	n/a	chr19:19627191-19627200
23	YY1	chr19:19626442-19627496	A549	lung:	n/a	chr19:19627191-19627200 chr19:19627043-19627055
24	POLR2A	chr19:19626227-19627353	GM12892	blood:	n/a	n/a
25	HEY1	chr19:19626418-19627474	K562	blood:	n/a	n/a
26	EP300	chr19:19626701-19627343	GM12878	blood:	n/a	n/a
27	MAX	chr19:19626464-19627497	A549	lung:	n/a	n/a
28	TCF12	chr19:19626597-19627470	ECC-1	luminal epithelium:	n/a	chr19:19626611-19626621 chr19:19626715-19626725
29	POLR2A	chr19:19626333-19627548	GM12891	blood:	n/a	n/a
30	POLR2A	chr19:19626543-19627428	HUVEC	blood vessel:	n/a	n/a
31	MAX	chr19:19626439-19627334	MCF-7	breast:	n/a	n/a
32	SIN3AK20	chr19:19626785-19627311	HepG2	liver:	n/a	n/a
33	POLR2A	chr19:19626708-19627351	K562	blood:	n/a	n/a
34	POLR2A	chr19:19626484-19627333	HepG2	liver:	n/a	n/a
35	GABPA	chr19:19626609-19627320	H1-hESC	embryonic stem cell:	n/a	chr19:19627191-19627200
36	SIN3AK20	chr19:19626252-19627723	MCF-7	breast:	n/a	n/a
37	POLR2A	chr19:19626423-19627369	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr19:19626370-19627456	GM12891	blood:	n/a	n/a
39	ELF1	chr19:19626251-19627641	HCT-116	colon:	n/a	chr19:19627019-19627032 chr19:19627249-19627261
40	POLR2A	chr19:19626516-19627449	HepG2	liver:	n/a	n/a
41	POLR2A	chr19:19625548-19627413	GM12892	blood:	n/a	n/a
42	RCOR1	chr19:19626390-19627433	HepG2	liver:	n/a	n/a
43	MXI1	chr19:19626661-19627426	HepG2	liver:	n/a	n/a
44	POLR2A	chr19:19625757-19627415	MCF-7	breast:	n/a	n/a
45	POLR2A	chr19:19626532-19627481	H1-neurons	neurons:	n/a	n/a
46	TAF1	chr19:19626545-19627546	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr19:19626514-19627421	GM12878	blood:	n/a	n/a
48	ELF1	chr19:19626514-19627384	MCF-7	breast:	n/a	chr19:19627019-19627032 chr19:19627249-19627261
49	POLR2A	chr19:19626043-19627328	GM12878	blood:	n/a	n/a
50	YY1	chr19:19626487-19627754	GM12892	blood:	n/a	chr19:19627191-19627200 chr19:19627043-19627055

No.	Distal block	Cell Line	Cell type
1	chr19:19625745..19628806-chr19:19639215..19643547,5	K562	blood:
2	chr19:19625773..19627404-chr19:19772860..19774540,2	MCF-7	breast:
3	chr19:19626939..19628497-chr19:19651278..19652936,2	K562	blood:
4	chr19:19301631..19304213-chr19:19625502..19628076,2	MCF-7	breast:
5	chr19:19625322..19628012-chr19:19773852..19776193,2	K562	blood:
6	chr19:19626852..19628495-chr19:19842334..19845203,2	MCF-7	breast:
7	chr19:19626804..19627575-chr3:48936168..48936977,2	Hela-S3	cervix:
8	chr19:19430154..19433018-chr19:19625258..19627975,2	K562	blood:
9	chr17:40975937..40976481-chr19:19627009..19627529,3	MCF-7	breast:
10	chr19:19625365..19628497-chr19:19651436..19653967,3	K562	blood:
11	chr19:19626484..19627370-chr2:28974167..28974761,2	HCT-116	colon:
12	chr19:19625980..19628021-chr19:19638084..19640231,2	K562	blood:
13	chr19:19622555..19628571-chr19:19737113..19740295,6	MCF-7	breast:
14	chr17:40975981..40976504-chr19:19627009..19627529,2	MCF-7	breast:
15	chr19:19625369..19628375-chr19:19648780..19652325,4	MCF-7	breast:
16	chr19:19625550..19627956-chr19:19752305..19756076,5	MCF-7	breast:
17	chr12:51611474..51612337-chr19:19626938..19627537,2	Hela-S3	cervix:

Variant related genes	Relation type
TSSK6	TF binding region
ENSG00000105708	Chromatin interaction
ENSG00000213639	Chromatin interaction
ENSG00000105705	Chromatin interaction
ENSG00000254901	Chromatin interaction
ENSG00000089639	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000129933	Chromatin interaction
ENSG00000105726	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000064489	Chromatin interaction
ENSG00000250067	Chromatin interaction
ENSG00000126581	Chromatin interaction
ENSG00000160161	Chromatin interaction
ENSG00000178537	Chromatin interaction
ENSG00000184271	Chromatin interaction
ENSG00000131467	Chromatin interaction
ENSG00000064547	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1036215	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10406278	0.83[EUR][1000 genomes]
rs11085264	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11668203	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11669558	0.96[EUR][1000 genomes]
rs11669730	0.88[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs11670687	0.98[EUR][1000 genomes]
rs11670761	0.99[EUR][1000 genomes]
rs11670775	1.00[CEU][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs11670882	0.88[ASW][hapmap];0.94[CEU][hapmap];0.94[LWK][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11671253	0.98[EUR][1000 genomes]
rs1529745	0.81[EUR][1000 genomes]
rs1560687	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs17684164	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2011503	1.00[CEU][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs2060274	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2060275	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2905434	0.82[EUR][1000 genomes]
rs2916070	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2916072	0.90[EUR][1000 genomes]
rs2916075	0.90[EUR][1000 genomes]
rs2965179	0.86[EUR][1000 genomes]
rs2965181	0.86[EUR][1000 genomes]
rs2965184	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs2965186	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs2965190	0.83[CEU][hapmap];0.93[TSI][hapmap]
rs2965195	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap]
rs2965201	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs34487417	0.84[EUR][1000 genomes]
rs34667451	0.98[EUR][1000 genomes]
rs45556231	0.99[EUR][1000 genomes]
rs45631651	0.99[EUR][1000 genomes]
rs4808204	0.98[EUR][1000 genomes]
rs4808205	0.99[EUR][1000 genomes]
rs4808206	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4808951	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4808958	0.84[EUR][1000 genomes]
rs4808962	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4808968	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4808969	0.99[EUR][1000 genomes]
rs4808970	0.98[EUR][1000 genomes]
rs55927782	0.99[EUR][1000 genomes]
rs56280531	0.98[EUR][1000 genomes]
rs56291054	0.84[EUR][1000 genomes]
rs56330647	1.00[EUR][1000 genomes]
rs58074958	0.90[EUR][1000 genomes]
rs61744761	0.96[EUR][1000 genomes]
rs7245689	1.00[EUR][1000 genomes]
rs7250233	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs7252453	0.94[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7256028	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs751857	0.83[GIH][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.98[EUR][1000 genomes]
rs754256	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs756997	1.00[CEU][hapmap]
rs8100927	0.99[EUR][1000 genomes]
rs8101219	0.99[EUR][1000 genomes]
rs8102502	0.94[CEU][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.95[EUR][1000 genomes]
rs8105642	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs8110171	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs8110250	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs8111093	0.82[EUR][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	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16996127	LSM4	cis	cerebellum	SCAN
rs16996127	GATAD2A	cis	parietal	SCAN
rs16996127	IL12RB1	cis	parietal	SCAN
rs16996127	JUND	cis	parietal	SCAN
rs16996127	OCEL1	cis	parietal	SCAN
rs16996127	SF4	Cis_1M	lymphoblastoid	RTeQTL
rs16996127	DDX49	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19624800-19627800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr19:19624800-19627800	Active TSS	Rectal Smooth Muscle	rectum
3	chr19:19624800-19628000	Active TSS	Fetal Kidney	kidney
4	chr19:19625200-19627800	Active TSS	Brain Hippocampus Middle	brain
5	chr19:19625800-19627600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:19626000-19628000	Active TSS	Hela-S3	cervix
7	chr19:19626200-19627800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:19626200-19627800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:19626200-19627800	Active TSS	HSMMtube	muscle
10	chr19:19626200-19628000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:19626200-19628200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr19:19626200-19628400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr19:19626200-19628400	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr19:19626200-19628400	Active TSS	A549	lung
15	chr19:19626200-19628400	Active TSS	HSMM	muscle
16	chr19:19626400-19627600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:19626400-19627600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:19626400-19627600	Active TSS	Aorta	Aorta
19	chr19:19626400-19627800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:19626400-19627800	Active TSS	Brain Substantia Nigra	brain
21	chr19:19626400-19627800	Active TSS	NHDF-Ad	bronchial
22	chr19:19626400-19628000	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr19:19626400-19628000	Active TSS	Right Atrium	heart
24	chr19:19626400-19628200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:19626400-19628200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr19:19626400-19628400	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr19:19626400-19628400	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr19:19626600-19627400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:19626600-19627400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
30	chr19:19626600-19627400	Active TSS	Spleen	Spleen
31	chr19:19626600-19627600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:19626600-19627600	Active TSS	Gastric	stomach
33	chr19:19626600-19627600	Bivalent/Poised TSS	HepG2	liver
34	chr19:19626600-19627800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:19626600-19627800	Active TSS	Brain Cingulate Gyrus	brain
36	chr19:19626600-19627800	Active TSS	Colon Smooth Muscle	Colon
37	chr19:19626600-19627800	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr19:19626600-19627800	Active TSS	Fetal Lung	lung
39	chr19:19626600-19627800	Active TSS	Left Ventricle	heart
40	chr19:19626600-19627800	Active TSS	Psoas Muscle	Psoas
41	chr19:19626600-19627800	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr19:19626600-19627800	Active TSS	Stomach Mucosa	stomach
43	chr19:19626600-19627800	Active TSS	NHEK	skin
44	chr19:19626600-19628000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr19:19626600-19628000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:19626600-19628000	Active TSS	Brain Angular Gyrus	brain
47	chr19:19626600-19628000	Active TSS	Brain Anterior Caudate	brain
48	chr19:19626600-19628000	Active TSS	Fetal Stomach	stomach
49	chr19:19626600-19628000	Active TSS	Ovary	ovary
50	chr19:19626600-19628000	Active TSS	Pancreas	Pancrea

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