Variant report

Variant	rs10425464
Chromosome Location	chr19:39325832-39325833
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39325351-39335703	K562	blood:	n/a	n/a
2	POLR2A	chr19:39325224-39327147	GM12891	blood:	n/a	n/a
3	POLR2A	chr19:39325327-39327188	K562	blood:	n/a	n/a
4	BCL3	chr19:39325179-39327051	A549	lung:	n/a	n/a
5	TCF12	chr19:39325816-39326620	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr19:39325825-39327117	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:39324470-39344503	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr19:39325826-39326312	HCT-116	colon:	n/a	n/a
9	POLR2A	chr19:39325377-39335667	A549	lung:	n/a	n/a
10	TCF12	chr19:39325292-39327031	A549	lung:	n/a	n/a
11	POLR2A	chr19:39325226-39343915	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:39325298-39335742	GM12892	blood:	n/a	n/a
13	POLR2A	chr19:39313168-39344379	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr19:39325268-39330971	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr19:39325690-39327058	SK-N-SH	brain:	n/a	n/a
16	SIN3AK20	chr19:39325169-39327064	PANC-1	pancreas:	n/a	n/a
17	GATA3	chr19:39325815-39326495	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr19:39325282-39327124	U87	brain:	n/a	n/a
19	POLR2A	chr19:39325772-39327036	HL-60	blood:	n/a	n/a
20	NFATC1	chr19:39325816-39326988	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:39325282-39327139	H1-hESC	embryonic stem cell:	n/a	n/a
22	MEF2A	chr19:39325808-39326565	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr19:39325170-39335506	H1-hESC	embryonic stem cell:	n/a	n/a
24	GATA3	chr19:39325171-39326780	A549	lung:	n/a	n/a
25	JUND	chr19:39325192-39327054	A549	lung:	n/a	chr19:39326312-39326324
26	POLR2A	chr19:39325377-39327062	GM12891	blood:	n/a	n/a
27	BCL3	chr19:39325180-39326963	A549	lung:	n/a	n/a
28	NFIC	chr19:39325832-39326628	SK-N-SH	brain:	n/a	n/a
29	EP300	chr19:39325808-39326917	A549	lung:	n/a	n/a
30	POLR2A	chr19:39325506-39327108	HepG2	liver:	n/a	n/a
31	POLR2A	chr19:39325370-39326186	A549	lung:	n/a	n/a
32	POLR2A	chr19:39325431-39327179	GM12891	blood:	n/a	n/a
33	POLR2A	chr19:39325336-39327122	MCF-7	breast:	n/a	n/a
34	POLR2A	chr19:39325825-39326515	A549	lung:	n/a	n/a
35	POLR2A	chr19:39325704-39335757	GM12892	blood:	n/a	n/a
36	POLR2A	chr19:39325223-39335761	GM12891	blood:	n/a	n/a
37	POLR2A	chr19:39325214-39330833	U87	brain:	n/a	n/a
38	POLR2A	chr19:39325625-39327610	PFSK-1	brain:	n/a	n/a
39	MEF2A	chr19:39325778-39326630	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr19:39325249-39326990	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr19:39325302-39335672	GM12892	blood:	n/a	n/a
42	POLR2A	chr19:39324475-39337293	SK-N-MC	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39221972..39229243-chr19:39319630..39326763,11	K562	blood:
2	chr19:39324931..39327493-chr19:39358939..39361060,2	MCF-7	breast:
3	chr19:39315714..39318484-chr19:39324884..39327703,2	K562	blood:
4	chr19:39218553..39228703-chr19:39324875..39331730,17	MCF-7	breast:
5	chr19:39325391..39328182-chr19:39375242..39377449,2	K562	blood:

No data

Variant related genes	Relation type
ECH1	TF binding region
ENSG00000187994	Chromatin interaction
ENSG00000267892	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000269050	Chromatin interaction
ENSG00000182472	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10403012	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10411480	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10411844	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1078734	0.88[AMR][1000 genomes]
rs11668179	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11668766	0.84[ASN][1000 genomes]
rs11671711	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12974488	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12977821	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075587	0.81[AMR][1000 genomes]
rs2075588	0.84[AMR][1000 genomes]
rs2116852	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2278010	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35829996	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4328569	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802928	0.82[EUR][1000 genomes]
rs7248208	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8110679	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs862454	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs862457	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs862458	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs862460	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs862461	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862462	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs862463	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9419	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9789283	0.82[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	nsv961291	chr19:39324891-39329561	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10425464	ECH1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39322400-39331800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39322600-39326200	Weak transcription	Gastric	stomach
3	chr19:39322600-39326400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:39322600-39326600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:39322600-39327400	Weak transcription	Small Intestine	intestine
6	chr19:39322800-39326200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:39322800-39326400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:39323000-39326000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:39323000-39326000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr19:39323000-39326000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:39323000-39326000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr19:39323000-39326000	Enhancers	Placenta	Placenta
13	chr19:39323000-39326200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:39323000-39326200	Weak transcription	Fetal Brain Male	brain
15	chr19:39323000-39326200	Weak transcription	Ovary	ovary
16	chr19:39323000-39327200	Weak transcription	Brain Angular Gyrus	brain
17	chr19:39323000-39334600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr19:39323200-39326000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:39323200-39326000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr19:39323200-39326000	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr19:39323200-39326000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr19:39323200-39326000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:39323200-39326000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:39323200-39326000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:39323200-39326000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:39323200-39326000	Weak transcription	Brain Hippocampus Middle	brain
27	chr19:39323200-39326000	Weak transcription	Colon Smooth Muscle	Colon
28	chr19:39323200-39326000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr19:39323200-39326000	Weak transcription	HSMM	muscle
30	chr19:39323200-39326000	Weak transcription	NH-A	brain
31	chr19:39323200-39326200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr19:39323200-39326200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr19:39323200-39326200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:39323200-39326200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr19:39323200-39326200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr19:39323200-39326200	Weak transcription	Brain Germinal Matrix	brain
37	chr19:39323200-39326200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:39323200-39326200	Weak transcription	Fetal Kidney	kidney
39	chr19:39323200-39326200	Weak transcription	Right Ventricle	heart
40	chr19:39323200-39326200	Weak transcription	GM12878-XiMat	blood
41	chr19:39323200-39326200	Weak transcription	Hela-S3	cervix
42	chr19:39323200-39326200	Weak transcription	HMEC	breast
43	chr19:39323200-39326200	Weak transcription	HSMMtube	muscle
44	chr19:39323200-39326200	Weak transcription	NHEK	skin
45	chr19:39323200-39326400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr19:39323200-39326400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr19:39323200-39326400	Weak transcription	NHLF	lung
48	chr19:39323200-39326600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr19:39323200-39326600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr19:39323200-39326600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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