Variant report

Variant	rs56330647
Chromosome Location	chr19:19627653-19627654
allele	A/G
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	YY1	chr19:19626349-19627656	H1-hESC	embryonic stem cell:	n/a	chr19:19627191-19627200 chr19:19627043-19627055
2	YY1	chr19:19626481-19627664	GM12878	blood:	n/a	chr19:19627191-19627200 chr19:19627043-19627055
3	SIN3AK20	chr19:19626252-19627723	MCF-7	breast:	n/a	n/a
4	YY1	chr19:19626487-19627754	GM12892	blood:	n/a	chr19:19627191-19627200 chr19:19627043-19627055
5	YY1	chr19:19626499-19627666	K562	blood:	n/a	chr19:19627191-19627200 chr19:19627043-19627055
6	YY1	chr19:19626411-19627744	GM12878	blood:	n/a	chr19:19627191-19627200 chr19:19627043-19627055
7	REST	chr19:19626445-19627654	H1-neurons	neurons:	n/a	n/a
8	ELF1	chr19:19625984-19627752	GM12878	blood:	n/a	chr19:19627019-19627032 chr19:19627249-19627261
9	GABPA	chr19:19626203-19627743	MCF-7	breast:	n/a	chr19:19627191-19627200 chr19:19627555-19627564
10	HA-E2F1	chr19:19626653-19627706	MCF-7	breast:	n/a	chr19:19626683-19626697 chr19:19627223-19627237 chr19:19627550-19627560 chr19:19627191-19627200
11	YY1	chr19:19626275-19627698	SK-N-SH	brain:	n/a	chr19:19627191-19627200 chr19:19627043-19627055
12	MXI1	chr19:19626426-19627774	IMR90	lung:	n/a	n/a
13	YY1	chr19:19626444-19627662	SK-N-SH	brain:	n/a	chr19:19627191-19627200 chr19:19627043-19627055
14	POLR2A	chr19:19627631-19627895	HepG2	liver:	n/a	n/a
15	MXI1	chr19:19626336-19627710	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19625745..19628806-chr19:19639215..19643547,5	K562	blood:
2	chr19:19626939..19628497-chr19:19651278..19652936,2	K562	blood:
3	chr19:19301631..19304213-chr19:19625502..19628076,2	MCF-7	breast:
4	chr19:19625322..19628012-chr19:19773852..19776193,2	K562	blood:
5	chr19:19626852..19628495-chr19:19842334..19845203,2	MCF-7	breast:
6	chr19:19430154..19433018-chr19:19625258..19627975,2	K562	blood:
7	chr19:19625365..19628497-chr19:19651436..19653967,3	K562	blood:
8	chr19:19625980..19628021-chr19:19638084..19640231,2	K562	blood:
9	chr19:19622555..19628571-chr19:19737113..19740295,6	MCF-7	breast:
10	chr19:19625369..19628375-chr19:19648780..19652325,4	MCF-7	breast:
11	chr19:19625550..19627956-chr19:19752305..19756076,5	MCF-7	breast:

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

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1036215	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10406278	0.83[EUR][1000 genomes]
rs11085264	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11668203	0.90[EUR][1000 genomes]
rs11669558	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11669730	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670687	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11670761	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670882	0.96[EUR][1000 genomes]
rs11671253	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1529745	0.81[EUR][1000 genomes]
rs1560687	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16996127	1.00[EUR][1000 genomes]
rs17684164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2060274	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2060275	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2905434	0.82[EUR][1000 genomes]
rs2916070	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2916072	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2916075	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2965179	0.86[EUR][1000 genomes]
rs2965181	0.86[EUR][1000 genomes]
rs2965184	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2965186	0.82[EUR][1000 genomes]
rs34487417	0.84[EUR][1000 genomes]
rs34667451	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs45556231	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs45631651	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808204	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4808205	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808206	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808951	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808958	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4808962	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4808968	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808969	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808970	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55927782	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56280531	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56291054	0.84[EUR][1000 genomes]
rs58074958	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61744761	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7245689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7250233	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7252453	0.97[EUR][1000 genomes]
rs7256028	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs751857	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs754256	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8100927	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8101219	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8102502	0.95[EUR][1000 genomes]
rs8105642	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8110171	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8110250	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56330647	SF4	Cis_1M	lymphoblastoid	RTeQTL

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	chr19:19626000-19628000	Active TSS	Hela-S3	cervix
6	chr19:19626200-19627800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:19626200-19627800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:19626200-19627800	Active TSS	HSMMtube	muscle
9	chr19:19626200-19628000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:19626200-19628200	Active TSS	H9 Cell Line	embryonic stem cell
11	chr19:19626200-19628400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr19:19626200-19628400	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr19:19626200-19628400	Active TSS	A549	lung
14	chr19:19626200-19628400	Active TSS	HSMM	muscle
15	chr19:19626400-19627800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:19626400-19627800	Active TSS	Brain Substantia Nigra	brain
17	chr19:19626400-19627800	Active TSS	NHDF-Ad	bronchial
18	chr19:19626400-19628000	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr19:19626400-19628000	Active TSS	Right Atrium	heart
20	chr19:19626400-19628200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:19626400-19628200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr19:19626400-19628400	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr19:19626400-19628400	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr19:19626600-19627800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:19626600-19627800	Active TSS	Brain Cingulate Gyrus	brain
26	chr19:19626600-19627800	Active TSS	Colon Smooth Muscle	Colon
27	chr19:19626600-19627800	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr19:19626600-19627800	Active TSS	Fetal Lung	lung
29	chr19:19626600-19627800	Active TSS	Left Ventricle	heart
30	chr19:19626600-19627800	Active TSS	Psoas Muscle	Psoas
31	chr19:19626600-19627800	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr19:19626600-19627800	Active TSS	Stomach Mucosa	stomach
33	chr19:19626600-19627800	Active TSS	NHEK	skin
34	chr19:19626600-19628000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr19:19626600-19628000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:19626600-19628000	Active TSS	Brain Angular Gyrus	brain
37	chr19:19626600-19628000	Active TSS	Brain Anterior Caudate	brain
38	chr19:19626600-19628000	Active TSS	Fetal Stomach	stomach
39	chr19:19626600-19628000	Active TSS	Ovary	ovary
40	chr19:19626600-19628000	Active TSS	Pancreas	Pancrea
41	chr19:19626600-19628000	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr19:19626600-19628000	Active TSS	GM12878-XiMat	blood
43	chr19:19626600-19628200	Active TSS	H1 Cell Line	embryonic stem cell
44	chr19:19626600-19628200	Active TSS	Colonic Mucosa	Colon
45	chr19:19626600-19628200	Active TSS	Small Intestine	intestine
46	chr19:19626600-19628200	Active TSS	NHLF	lung
47	chr19:19626600-19628400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr19:19626600-19628600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr19:19626600-19628600	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr19:19626800-19627800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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