Variant report

Variant	rs10403012
Chromosome Location	chr19:39330058-39330059
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	POLR2A	chr19:39325351-39335703	K562	blood:	n/a	n/a
2	POLR2A	chr19:39327178-39330434	GM12892	blood:	n/a	n/a
3	POLR2A	chr19:39327275-39334537	K562	blood:	n/a	n/a
4	POLR2A	chr19:39329108-39330483	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr19:39327201-39331578	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr19:39328436-39330878	HL-60	blood:	n/a	n/a
7	POLR2A	chr19:39329889-39330293	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr19:39324470-39344503	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr19:39329912-39330129	A549	lung:	n/a	n/a
10	POLR2A	chr19:39325896-39330910	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:39328323-39330685	HepG2	liver:	n/a	n/a
12	HEY1	chr19:39328842-39330408	K562	blood:	n/a	n/a
13	POLR2A	chr19:39325377-39335667	A549	lung:	n/a	n/a
14	POLR2A	chr19:39325226-39343915	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:39327254-39335682	GM12891	blood:	n/a	n/a
16	POLR2A	chr19:39325298-39335742	GM12892	blood:	n/a	n/a
17	POLR2A	chr19:39313168-39344379	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr19:39329167-39330503	HL-60	blood:	n/a	n/a
19	POLR2A	chr19:39329903-39330110	HepG2	liver:	n/a	n/a
20	POLR2A	chr19:39325268-39330971	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr19:39327162-39334961	HCT-116	colon:	n/a	n/a
22	POLR2A	chr19:39328679-39330693	GM18505	blood:	n/a	n/a
23	POLR2A	chr19:39327993-39331050	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr19:39328551-39330759	GM19193	blood:	n/a	n/a
25	POLR2A	chr19:39329715-39330085	U87	brain:	n/a	n/a
26	POLR2A	chr19:39329153-39330210	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr19:39328441-39330437	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:39328511-39330323	PBDE	blood:	n/a	n/a
29	POLR2A	chr19:39327320-39335679	K562	blood:	n/a	n/a
30	POLR2A	chr19:39327286-39330419	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr19:39325170-39335506	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr19:39327277-39331126	K562	blood:	n/a	n/a
33	BCL3	chr19:39327233-39330842	A549	lung:	n/a	chr19:39328370-39328379
34	POLR2A	chr19:39327445-39330729	GM12878	blood:	n/a	n/a
35	SIN3AK20	chr19:39328100-39330837	PANC-1	pancreas:	n/a	n/a
36	POLR2A	chr19:39327155-39330483	GM12891	blood:	n/a	n/a
37	POLR2A	chr19:39328299-39330492	MCF-7	breast:	n/a	n/a
38	POLR2A	chr19:39327311-39330651	GM12891	blood:	n/a	n/a
39	BCL3	chr19:39329044-39330454	A549	lung:	n/a	n/a
40	POLR2A	chr19:39327305-39332837	K562	blood:	n/a	n/a
41	POLR2A	chr19:39329727-39330234	SK-N-SH	brain:	n/a	n/a
42	JUND	chr19:39329021-39330882	HCT-116	colon:	n/a	chr19:39330612-39330622 chr19:39329364-39329374 chr19:39330612-39330622 chr19:39329425-39329437 chr19:39330613-39330621 chr19:39330612-39330622 chr19:39329365-39329373 chr19:39329364-39329374 chr19:39330612-39330622 chr19:39329363-39329375
43	POLR2A	chr19:39329848-39330421	H1-neurons	neurons:	n/a	n/a
44	POLR2A	chr19:39329837-39330271	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr19:39327191-39330839	U87	brain:	n/a	n/a
46	POLR2A	chr19:39329515-39330362	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr19:39329785-39330128	GM12878	blood:	n/a	n/a
48	POLR2A	chr19:39327229-39330473	HepG2	liver:	n/a	n/a
49	JUND	chr19:39329140-39330821	HCT-116	colon:	n/a	chr19:39330612-39330622 chr19:39329364-39329374 chr19:39330612-39330622 chr19:39329425-39329437 chr19:39330613-39330621 chr19:39330612-39330622 chr19:39329365-39329373 chr19:39329364-39329374 chr19:39330612-39330622 chr19:39329363-39329375
50	POLR2A	chr19:39329246-39330088	GM18951	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39303539..39306224-chr19:39328570..39331543,2	MCF-7	breast:
2	chr19:39216544..39219007-chr19:39328306..39331285,2	MCF-7	breast:
3	chr19:39137584..39140325-chr19:39327324..39331607,4	MCF-7	breast:
4	chr19:39218553..39228703-chr19:39324875..39331730,17	MCF-7	breast:
5	chr19:39137231..39139589-chr19:39329369..39331157,2	MCF-7	breast:
6	chr19:39223964..39228282-chr19:39327392..39332302,8	MCF-7	breast:

Variant related genes	Relation type
HNRNPL	TF binding region
ENSG00000182472	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000171747	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10411480	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10411844	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10424892	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs10425464	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1078734	0.84[CEU][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11668179	0.95[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11668766	0.88[CHD][hapmap];0.84[JPT][hapmap]
rs11671711	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12974488	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12977821	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1529713	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs2075588	0.87[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs2116852	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2278010	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35829996	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4328569	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802928	0.82[EUR][1000 genomes]
rs7248208	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8108906	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs8110679	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs862454	0.92[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs862457	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs862458	0.92[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs862460	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs862461	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs862462	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs862463	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9419	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]

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	nsv961215	chr19:39329561-39331790	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10403012	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	chr19:39323000-39334600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:39324600-39338000	Strong transcription	Fetal Brain Female	brain
4	chr19:39325000-39334000	Strong transcription	Fetal Stomach	stomach
5	chr19:39325200-39331600	Strong transcription	Primary T cells from cord blood	blood
6	chr19:39325400-39331200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr19:39325400-39331600	Strong transcription	Fetal Thymus	thymus
8	chr19:39325400-39332000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:39325400-39332200	Strong transcription	Thymus	Thymus
10	chr19:39325400-39336800	Strong transcription	Brain Substantia Nigra	brain
11	chr19:39325400-39337800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:39325400-39337800	Strong transcription	Brain Cingulate Gyrus	brain
13	chr19:39325400-39338000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:39325400-39338200	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr19:39325400-39338200	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr19:39325600-39333600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:39325600-39338000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:39325800-39330800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:39326000-39331000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr19:39326000-39331200	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr19:39326000-39332200	Genic enhancers	Placenta	Placenta
22	chr19:39326000-39332600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:39326000-39332600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr19:39326000-39333800	Strong transcription	Colonic Mucosa	Colon
25	chr19:39326000-39334000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:39326000-39336200	Strong transcription	Brain Hippocampus Middle	brain
27	chr19:39326000-39336600	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr19:39326000-39337000	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr19:39326000-39337800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:39326000-39338000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:39326000-39338000	Strong transcription	Brain Anterior Caudate	brain
32	chr19:39326000-39338000	Strong transcription	HSMM	muscle
33	chr19:39326000-39338200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr19:39326000-39338200	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr19:39326000-39338200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:39326000-39338200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr19:39326000-39338200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr19:39326000-39338400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
39	chr19:39326000-39338400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr19:39326000-39338600	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr19:39326200-39330400	Genic enhancers	Stomach Mucosa	stomach
42	chr19:39326200-39330600	Genic enhancers	Hela-S3	cervix
43	chr19:39326200-39331400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr19:39326200-39331600	Strong transcription	Primary B cells from cord blood	blood
45	chr19:39326200-39331600	Strong transcription	Adipose Nuclei	Adipose
46	chr19:39326200-39331800	Strong transcription	GM12878-XiMat	blood
47	chr19:39326200-39332800	Genic enhancers	HMEC	breast
48	chr19:39326200-39333200	Strong transcription	Dnd41	blood
49	chr19:39326200-39333800	Strong transcription	Brain Germinal Matrix	brain
50	chr19:39326200-39334600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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