Variant report

Variant	rs17684164
Chromosome Location	chr19:19626769-19626770
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	chr19:19626720-19626870	HEK293	kidney:	n/a	n/a
2	POLR2A	chr19:19626623-19627292	U87	brain:	n/a	n/a
3	MYC	chr19:19626720-19627165	H1-hESC	embryonic stem cell:	n/a	n/a
4	TAF1	chr19:19626719-19627446	PFSK-1	brain:	n/a	n/a
5	JUND	chr19:19626406-19627464	K562	blood:	n/a	chr19:19626492-19626501 chr19:19626491-19626502
6	E2F6	chr19:19626620-19627185	A549	lung:	n/a	chr19:19626683-19626697 chr19:19626902-19626913
7	POLR2A	chr19:19626458-19627436	K562	blood:	n/a	n/a
8	YY1	chr19:19626632-19627267	GM12891	blood:	n/a	chr19:19627191-19627200 chr19:19627043-19627055
9	YY1	chr19:19626349-19627656	H1-hESC	embryonic stem cell:	n/a	chr19:19627191-19627200 chr19:19627043-19627055
10	MAX	chr19:19626465-19627353	ECC-1	luminal epithelium:	n/a	n/a
11	NRF1	chr19:19626532-19626854	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr19:19626559-19627404	ProgFib	skin:	n/a	n/a
13	RELA	chr19:19626729-19627422	GM19193	blood:	n/a	n/a
14	YY1	chr19:19626481-19627664	GM12878	blood:	n/a	chr19:19627191-19627200 chr19:19627043-19627055
15	MYC	chr19:19626566-19627585	NB4	blood:	n/a	chr19:19627553-19627563
16	ELK1	chr19:19626582-19627234	Hela-S3	cervix:	n/a	n/a
17	YY1	chr19:19626584-19627260	K562	blood:	n/a	chr19:19627191-19627200 chr19:19627043-19627055
18	POLR2A	chr19:19626733-19627326	HEK293	kidney:	n/a	n/a
19	POLR2A	chr19:19626458-19627312	GM12892	blood:	n/a	n/a
20	POLR2A	chr19:19626512-19627307	NB4	blood:	n/a	n/a
21	PML	chr19:19626533-19627151	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:19626408-19627482	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr19:19626738-19627317	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:19626696-19627326	H1-hESC	embryonic stem cell:	n/a	n/a
25	TBP	chr19:19626660-19627425	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:19626716-19627178	HepG2	liver:	n/a	n/a
27	IRF1	chr19:19626759-19627443	K562	blood:	n/a	chr19:19627244-19627258 chr19:19627190-19627204
28	MAZ	chr19:19626482-19627477	GM12878	blood:	n/a	n/a
29	NFIC	chr19:19626728-19627152	HepG2	liver:	n/a	n/a
30	ELK4	chr19:19626444-19627311	Hela-S3	cervix:	n/a	chr19:19627022-19627033 chr19:19627007-19627018
31	GTF2F1	chr19:19626750-19627176	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr19:19626603-19627288	A549	lung:	n/a	n/a
33	E2F6	chr19:19626761-19627044	K562	blood:	n/a	chr19:19626902-19626913
34	MAX	chr19:19626685-19627224	Hela-S3	cervix:	n/a	n/a
35	ELF1	chr19:19626561-19627318	SK-N-SH	brain:	n/a	chr19:19627019-19627032 chr19:19627249-19627261
36	POLR2A	chr19:19626400-19627444	HCT-116	colon:	n/a	n/a
37	TAF1	chr19:19626716-19627437	SK-N-SH	brain:	n/a	n/a
38	GABPA	chr19:19626433-19627384	K562	blood:	n/a	chr19:19627191-19627200
39	YY1	chr19:19626442-19627496	A549	lung:	n/a	chr19:19627191-19627200 chr19:19627043-19627055
40	POLR2A	chr19:19626227-19627353	GM12892	blood:	n/a	n/a
41	NFATC1	chr19:19626712-19627106	GM12878	blood:	n/a	n/a
42	STAT5A	chr19:19626662-19627182	GM12878	blood:	n/a	n/a
43	HEY1	chr19:19626418-19627474	K562	blood:	n/a	n/a
44	ELF1	chr19:19626539-19627259	HepG2	liver:	n/a	chr19:19627019-19627032
45	EP300	chr19:19626701-19627343	GM12878	blood:	n/a	n/a
46	MAX	chr19:19626464-19627497	A549	lung:	n/a	n/a
47	TCF12	chr19:19626597-19627470	ECC-1	luminal epithelium:	n/a	chr19:19626611-19626621 chr19:19626715-19626725
48	POLR2A	chr19:19626333-19627548	GM12891	blood:	n/a	n/a
49	CEBPD	chr19:19626690-19627290	K562	blood:	n/a	n/a
50	POLR2A	chr19:19626543-19627428	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19625745..19628806-chr19:19639215..19643547,5	K562	blood:
2	chr19:19626434..19626951-chr7:72971933..72972539,2	Hela-S3	cervix:
3	chr19:19625773..19627404-chr19:19772860..19774540,2	MCF-7	breast:
4	chr19:19626216..19626994-chr3:152879483..152880164,3	Hela-S3	cervix:
5	chr17:62658184..62658718-chr19:19626329..19627292,2	Hela-S3	cervix:
6	chr19:19301631..19304213-chr19:19625502..19628076,2	MCF-7	breast:
7	chr19:19625322..19628012-chr19:19773852..19776193,2	K562	blood:
8	chr19:19430154..19433018-chr19:19625258..19627975,2	K562	blood:
9	chr19:19625365..19628497-chr19:19651436..19653967,3	K562	blood:
10	chr19:19626484..19627370-chr2:28974167..28974761,2	HCT-116	colon:
11	chr19:19625980..19628021-chr19:19638084..19640231,2	K562	blood:
12	chr19:19622555..19628571-chr19:19737113..19740295,6	MCF-7	breast:
13	chr19:19625665..19627306-chr19:19648287..19650892,2	K562	blood:
14	chr19:19625369..19628375-chr19:19648780..19652325,4	MCF-7	breast:
15	chr19:19625550..19627956-chr19:19752305..19756076,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258674	TF binding region
NDUFA13	TF binding region
TSSK6	TF binding region
YJEFN3	TF binding region
ENSG00000129933	Chromatin interaction
ENSG00000089639	Chromatin interaction
ENSG00000105726	Chromatin interaction
ENSG00000160161	Chromatin interaction
ENSG00000108854	Chromatin interaction
ENSG00000213639	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000105705	Chromatin interaction
ENSG00000244268	Chromatin interaction
ENSG00000064489	Chromatin interaction
ENSG00000250067	Chromatin interaction
ENSG00000181467	Chromatin interaction
ENSG00000106635	Chromatin interaction
ENSG00000254901	Chromatin interaction
ENSG00000213999	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1036215	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10406278	0.83[EUR][1000 genomes]
rs11085264	1.00[CEU][hapmap];1.00[YRI][hapmap];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	0.88[CEU][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670687	0.93[YRI][hapmap];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	1.00[CEU][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11670882	0.94[CEU][hapmap];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	1.00[CEU][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16996127	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2011503	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs2060274	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2060275	1.00[CEU][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2905434	0.82[EUR][1000 genomes]
rs2916070	1.00[CEU][hapmap];0.85[YRI][hapmap];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	1.00[CEU][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2965186	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes]
rs2965190	0.82[CEU][hapmap]
rs2965195	1.00[CEU][hapmap]
rs2965201	1.00[CEU][hapmap];0.93[YRI][hapmap]
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	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4808951	1.00[CEU][hapmap];0.93[YRI][hapmap];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	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4808968	1.00[CEU][hapmap];0.93[YRI][hapmap];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]
rs56330647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	1.00[CEU][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7252453	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs7256028	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs751857	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs754256	1.00[CEU][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs756997	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs8100927	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8101219	0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8102502	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs8105642	1.00[CEU][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8110171	1.00[CEU][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8110250	1.00[CEU][hapmap];0.93[YRI][hapmap];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
rs17684164	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	chr19:19625800-19627600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:19626000-19626800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr19:19626000-19626800	Flanking Active TSS	Liver	Liver
8	chr19:19626000-19628000	Active TSS	Hela-S3	cervix
9	chr19:19626200-19626800	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr19:19626200-19626800	Flanking Active TSS	Primary B cells from peripheral blood	blood
11	chr19:19626200-19626800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
12	chr19:19626200-19626800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr19:19626200-19626800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr19:19626200-19626800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr19:19626200-19626800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr19:19626200-19626800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr19:19626200-19626800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr19:19626200-19626800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:19626200-19626800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:19626200-19626800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:19626200-19626800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:19626200-19626800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:19626200-19626800	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr19:19626200-19626800	Flanking Active TSS	Fetal Brain Female	brain
25	chr19:19626200-19626800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr19:19626200-19626800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr19:19626200-19626800	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr19:19626200-19627800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr19:19626200-19627800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr19:19626200-19627800	Active TSS	HSMMtube	muscle
31	chr19:19626200-19628000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:19626200-19628200	Active TSS	H9 Cell Line	embryonic stem cell
33	chr19:19626200-19628400	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr19:19626200-19628400	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr19:19626200-19628400	Active TSS	A549	lung
36	chr19:19626200-19628400	Active TSS	HSMM	muscle
37	chr19:19626400-19626800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:19626400-19626800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:19626400-19626800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:19626400-19626800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:19626400-19626800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:19626400-19626800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr19:19626400-19626800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr19:19626400-19626800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:19626400-19626800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:19626400-19626800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr19:19626400-19626800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr19:19626400-19626800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr19:19626400-19626800	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr19:19626400-19626800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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