Variant report

Variant	rs9419
Chromosome Location	chr19:39322087-39322088
allele	A/C
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	SMC3	chr19:39321812-39322800	GM12878	blood:	n/a	n/a
2	TAF1	chr19:39321869-39322839	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr19:39321808-39322139	HepG2	liver:	n/a	n/a
4	ZNF217	chr19:39321760-39322839	MCF-7	breast:	n/a	n/a
5	YY1	chr19:39321751-39322975	SK-N-SH	brain:	n/a	chr19:39322483-39322505 chr19:39322461-39322475 chr19:39322413-39322422 chr19:39322482-39322494 chr19:39322542-39322564 chr19:39322486-39322494 chr19:39322543-39322551 chr19:39322540-39322559 chr19:39322819-39322829 chr19:39322542-39322552 chr19:39322545-39322553 chr19:39322483-39322493
6	MAX	chr19:39321765-39322757	HepG2	liver:	n/a	chr19:39322464-39322474
7	MBD4	chr19:39321764-39322901	HepG2	liver:	n/a	n/a
8	MXI1	chr19:39321816-39322744	GM12878	blood:	n/a	n/a
9	SIN3AK20	chr19:39321587-39323048	A549	lung:	n/a	n/a
10	GATA3	chr19:39321709-39322364	MCF-7	breast:	n/a	n/a
11	GABPA	chr19:39321817-39323087	A549	lung:	n/a	n/a
12	MAX	chr19:39321675-39322905	ECC-1	luminal epithelium:	n/a	chr19:39322464-39322474
13	POLR2A	chr19:39321916-39322916	GM12892	blood:	n/a	n/a
14	POLR2A	chr19:39321611-39322751	HepG2	liver:	n/a	n/a
15	POLR2A	chr19:39321802-39322738	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:39321561-39322816	GM12891	blood:	n/a	n/a
17	YY1	chr19:39321811-39322989	ECC-1	luminal epithelium:	n/a	chr19:39322483-39322505 chr19:39322461-39322475 chr19:39322413-39322422 chr19:39322482-39322494 chr19:39322542-39322564 chr19:39322486-39322494 chr19:39322543-39322551 chr19:39322540-39322559 chr19:39322819-39322829 chr19:39322542-39322552 chr19:39322545-39322553 chr19:39322483-39322493
18	BCLAF1	chr19:39321931-39322895	GM12878	blood:	n/a	chr19:39322784-39322792
19	ARID3A	chr19:39322019-39322821	K562	blood:	n/a	n/a
20	POLR2A	chr19:39321909-39322838	K562	blood:	n/a	n/a
21	EP300	chr19:39321944-39322877	HepG2	liver:	n/a	chr19:39322776-39322786
22	KAP1	chr19:39322079-39323033	U2OS	brain:	n/a	n/a
23	POLR2A	chr19:39321934-39322892	K562	blood:	n/a	n/a
24	MAFK	chr19:39321815-39322719	IMR90	lung:	n/a	n/a
25	RFX5	chr19:39321893-39322820	GM12878	blood:	n/a	chr19:39322709-39322724
26	BHLHE40	chr19:39321707-39323235	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:39321374-39323387	HepG2	liver:	n/a	n/a
28	TEAD4	chr19:39321725-39322274	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr19:39321842-39323062	HUVEC	blood vessel:	n/a	n/a
30	ELF1	chr19:39321835-39322224	HepG2	liver:	n/a	n/a
31	REST	chr19:39321728-39322861	PFSK-1	brain:	n/a	n/a
32	MBD4	chr19:39322071-39322974	HepG2	liver:	n/a	n/a
33	YY1	chr19:39321619-39322987	SK-N-SH_RA	brain:	n/a	chr19:39322483-39322505 chr19:39322461-39322475 chr19:39322413-39322422 chr19:39322482-39322494 chr19:39322542-39322564 chr19:39322486-39322494 chr19:39322543-39322551 chr19:39322540-39322559 chr19:39322819-39322829 chr19:39322542-39322552 chr19:39322545-39322553 chr19:39322483-39322493
34	MAX	chr19:39321876-39322587	H1-hESC	embryonic stem cell:	n/a	chr19:39322464-39322474
35	MAX	chr19:39321874-39322718	K562	blood:	n/a	chr19:39322464-39322474
36	POLR2A	chr19:39321891-39322890	MCF10A-Er-Src	breast:	n/a	n/a
37	TAF1	chr19:39321841-39322870	GM12878	blood:	n/a	n/a
38	YY1	chr19:39321792-39322971	HepG2	liver:	n/a	chr19:39322483-39322505 chr19:39322461-39322475 chr19:39322413-39322422 chr19:39322482-39322494 chr19:39322542-39322564 chr19:39322486-39322494 chr19:39322543-39322551 chr19:39322540-39322559 chr19:39322819-39322829 chr19:39322542-39322552 chr19:39322545-39322553 chr19:39322483-39322493
39	POLR2A	chr19:39321923-39322685	GM12891	blood:	n/a	n/a
40	MAZ	chr19:39321474-39323120	IMR90	lung:	n/a	chr19:39322464-39322474
41	EGR1	chr19:39321843-39322935	HCT-116	colon:	n/a	chr19:39322463-39322473 chr19:39321902-39321912 chr19:39322460-39322475 chr19:39322461-39322474
42	MAFK	chr19:39321895-39322111	HepG2	liver:	n/a	n/a
43	ZNF143	chr19:39321792-39322730	K562	blood:	n/a	chr19:39321904-39321922
44	BHLHE40	chr19:39321849-39322700	GM12878	blood:	n/a	n/a
45	ELF1	chr19:39321833-39322883	A549	lung:	n/a	chr19:39322461-39322473 chr19:39322413-39322422
46	ZNF263	chr19:39321852-39322659	HEK293-T-REx	kidney:	n/a	n/a
47	YY1	chr19:39321937-39322969	H1-hESC	embryonic stem cell:	n/a	chr19:39322483-39322505 chr19:39322461-39322475 chr19:39322413-39322422 chr19:39322482-39322494 chr19:39322542-39322564 chr19:39322486-39322494 chr19:39322543-39322551 chr19:39322540-39322559 chr19:39322819-39322829 chr19:39322542-39322552 chr19:39322545-39322553 chr19:39322483-39322493
48	POLR2A	chr19:39321606-39322874	PFSK-1	brain:	n/a	n/a
49	TAF1	chr19:39322044-39322826	GM12891	blood:	n/a	n/a
50	POLR2A	chr19:39320432-39324423	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39221972..39229243-chr19:39319630..39326763,11	K562	blood:
2	chr19:39225035..39229236-chr19:39320225..39324035,5	K562	blood:
3	chr19:39305126..39308258-chr19:39321941..39324366,4	K562	blood:
4	chr19:39138022..39142840-chr19:39322070..39325450,5	MCF-7	breast:
5	chr19:39224613..39228237-chr19:39319464..39324480,6	MCF-7	breast:
6	chr19:39137520..39139996-chr19:39320132..39324117,5	MCF-7	breast:
7	chr19:39320984..39323718-chr19:39390338..39392657,3	K562	blood:
8	chr19:39322011..39322549-chr7:45150885..45151612,2	Hela-S3	cervix:
9	chr19:10362582..10363540-chr19:39322006..39323005,2	NB4	blood:
10	chr19:39321462..39323411-chr19:39359373..39361824,2	MCF-7	breast:
11	chr19:39292786..39294819-chr19:39320796..39322447,2	MCF-7	breast:

Variant related genes	Relation type
ECH1	TF binding region
ENSG00000187994	Chromatin interaction
ENSG00000267892	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000104823	Chromatin interaction
ENSG00000136270	Chromatin interaction
ENSG00000104825	Chromatin interaction
ENSG00000068903	Chromatin interaction
ENSG00000171747	Chromatin interaction
ENSG00000269050	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000105364	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10403012	0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10411480	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10411844	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10424892	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs10425464	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10426289	0.85[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1078734	0.85[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11668179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs11668766	0.97[CHD][hapmap];0.83[JPT][hapmap]
rs11671711	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12974488	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12977821	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1529713	0.95[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs2075587	0.81[AMR][1000 genomes]
rs2075588	0.84[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2113123	0.85[JPT][hapmap]
rs2116852	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2278010	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28496951	0.85[JPT][hapmap]
rs35829996	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4328569	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802928	0.82[EUR][1000 genomes]
rs7248208	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8104420	0.85[JPT][hapmap]
rs8108906	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs8110679	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs862454	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs862457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs862458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs862460	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs862461	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs862462	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs862463	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][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	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv911670	chr19:39250308-39322087	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9419	ECH1	Cis_1M	lymphoblastoid	RTeQTL
rs9419	ENSG00000104823	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39320200-39322400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr19:39320400-39322200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr19:39320800-39322200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:39321000-39322400	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr19:39321200-39322200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr19:39321400-39322200	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr19:39321400-39322200	Flanking Active TSS	Fetal Heart	heart
8	chr19:39321400-39322200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr19:39321400-39322200	Flanking Active TSS	Dnd41	blood
10	chr19:39321400-39322400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:39321400-39322400	Flanking Active TSS	Placenta	Placenta
12	chr19:39321400-39322400	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr19:39321400-39322800	Active TSS	Brain Anterior Caudate	brain
14	chr19:39321400-39323000	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr19:39321400-39323000	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr19:39321400-39323000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr19:39321600-39322200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
18	chr19:39321600-39322200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:39321600-39322200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr19:39321600-39322200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr19:39321600-39322200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:39321600-39322200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr19:39321600-39322200	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr19:39321600-39322200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr19:39321600-39322200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:39321600-39322200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr19:39321600-39322200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr19:39321600-39322200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:39321600-39322200	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr19:39321600-39322200	Flanking Active TSS	Fetal Brain Male	brain
31	chr19:39321600-39322200	Flanking Active TSS	Fetal Brain Female	brain
32	chr19:39321600-39322200	Flanking Active TSS	Fetal Thymus	thymus
33	chr19:39321600-39322200	Flanking Active TSS	Rectal Smooth Muscle	rectum
34	chr19:39321600-39322200	Flanking Active TSS	NHDF-Ad	bronchial
35	chr19:39321600-39322400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:39321600-39322400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr19:39321600-39322400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr19:39321600-39322400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
39	chr19:39321600-39322400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:39321600-39322400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:39321600-39322400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr19:39321600-39322400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:39321600-39322400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr19:39321600-39322400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:39321600-39322400	Flanking Active TSS	HSMM	muscle
46	chr19:39321600-39322400	Flanking Active TSS	HUVEC	blood vessel
47	chr19:39321600-39322400	Flanking Active TSS	NH-A	brain
48	chr19:39321600-39322400	Flanking Active TSS	NHLF	lung
49	chr19:39321600-39322600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr19:39321600-39322600	Active TSS	HUES48 Cell Line	embryonic stem cell

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