Variant report

Variant	rs34406232
Chromosome Location	chr19:41305530-41305531
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	EGR1	chr19:41305518-41305746	GM12878	blood:	n/a	chr19:41305645-41305659 chr19:41305648-41305661
2	STAT5A	chr19:41305235-41305736	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:41304000-41305727	K562	blood:	n/a	n/a
4	TAF1	chr19:41305417-41305785	K562	blood:	n/a	n/a
5	CHD2	chr19:41305154-41305574	H1-hESC	embryonic stem cell:	n/a	n/a
6	MYC	chr19:41303973-41305666	K562	blood:	n/a	chr19:41305045-41305054 chr19:41305044-41305055 chr19:41304746-41304756
7	POLR2A	chr19:41305385-41305743	GM12891	blood:	n/a	n/a
8	EGR1	chr19:41304580-41305859	K562	blood:	n/a	chr19:41305808-41305818 chr19:41304834-41304849 chr19:41305810-41305820 chr19:41304745-41304755 chr19:41304748-41304761 chr19:41305086-41305100 chr19:41304888-41304898 chr19:41305810-41305823 chr19:41304883-41304896 chr19:41305645-41305659 chr19:41305015-41305024 chr19:41305648-41305661
9	POLR2A	chr19:41304007-41306203	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr19:41304005-41305758	GM12892	blood:	n/a	n/a
11	JUND	chr19:41305478-41305615	K562	blood:	n/a	n/a
12	EP300	chr19:41304115-41305703	K562	blood:	n/a	chr19:41305138-41305147 chr19:41305137-41305146
13	TCF12	chr19:41303652-41306370	A549	lung:	n/a	chr19:41304331-41304341 chr19:41305722-41305732 chr19:41304332-41304339 chr19:41306069-41306076
14	TBL1XR1	chr19:41305274-41305770	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:41305365-41305730	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr19:41304266-41305794	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr19:41303846-41305786	HL-60	blood:	n/a	n/a
18	GABPA	chr19:41305321-41305800	K562	blood:	n/a	n/a
19	POLR2A	chr19:41305425-41305660	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr19:41304604-41305757	ProgFib	skin:	n/a	n/a
21	TAF1	chr19:41304859-41305684	HepG2	liver:	n/a	n/a
22	POLR2A	chr19:41303823-41306482	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr19:41303926-41305652	GM12878	blood:	n/a	n/a
24	HEY1	chr19:41305391-41305695	K562	blood:	n/a	n/a
25	POLR2A	chr19:41303962-41305722	GM18526	blood:	n/a	n/a
26	MTA3	chr19:41305369-41305748	GM12878	blood:	n/a	n/a
27	SIN3A	chr19:41305417-41305666	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:41305465-41305731	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr19:41303903-41305756	Hela-S3	cervix:	n/a	n/a
30	MAX	chr19:41303865-41305816	K562	blood:	n/a	chr19:41305045-41305054 chr19:41305044-41305055 chr19:41304746-41304756
31	POLR2A	chr19:41303968-41305765	GM18951	blood:	n/a	n/a
32	REST	chr19:41303932-41306015	H1-neurons	neurons:	n/a	chr19:41304173-41304193 chr19:41304745-41304758
33	POLR2A	chr19:41303795-41305758	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr19:41303782-41305823	GM12892	blood:	n/a	n/a
35	MAX	chr19:41305500-41305640	GM12878	blood:	n/a	n/a
36	BHLHE40	chr19:41303923-41305731	GM12878	blood:	n/a	chr19:41305046-41305055 chr19:41305045-41305054 chr19:41304477-41304493 chr19:41305045-41305054 chr19:41305044-41305053 chr19:41305043-41305056
37	UBTF	chr19:41305101-41306121	K562	blood:	n/a	n/a
38	JUND	chr19:41303907-41305834	A549	lung:	n/a	chr19:41304752-41304761 chr19:41304797-41304806 chr19:41305806-41305815
39	SIX5	chr19:41305491-41306433	A549	lung:	n/a	n/a
40	POLR2A	chr19:41303927-41305727	GM18505	blood:	n/a	n/a
41	POLR2A	chr19:41303975-41306078	K562	blood:	n/a	n/a
42	MYC	chr19:41305287-41305536	K562	blood:	n/a	n/a
43	TAF1	chr19:41305357-41305725	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr19:41305368-41305732	K562	blood:	n/a	n/a
45	POLR2A	chr19:41303966-41305738	GM15510	blood:	n/a	n/a
46	GABPA	chr19:41305510-41305724	HepG2	liver:	n/a	n/a
47	POLR2A	chr19:41304477-41305778	A549	lung:	n/a	n/a
48	MXI1	chr19:41303661-41306345	SK-N-SH	brain:	n/a	n/a
49	YY1	chr19:41304031-41305679	K562	blood:	n/a	chr19:41304477-41304488 chr19:41305138-41305147 chr19:41304888-41304897 chr19:41304471-41304485 chr19:41305138-41305152 chr19:41305011-41305025
50	POLR2A	chr19:41305390-41305735	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41280731..41296556-chr19:41299561..41307605,30	MCF-7	breast:
2	chr19:41187113..41189368-chr19:41304406..41306617,2	K562	blood:
3	chr19:41254487..41259247-chr19:41302579..41309995,18	K562	blood:
4	chr19:41266506..41270324-chr19:41304182..41308237,4	MCF-7	breast:
5	chr19:41304966..41305637-chr9:33025041..33025768,2	Hela-S3	cervix:
6	chr19:41281732..41286442-chr19:41302482..41306628,13	K562	blood:
7	chr19:41303143..41305588-chr19:41428304..41431722,3	MCF-7	breast:
8	chr19:41254747..41256268-chr19:41303480..41305851,2	MCF-7	breast:
9	chr19:41281718..41286533-chr19:41301356..41311124,20	K562	blood:
10	chr19:41221300..41223743-chr19:41303378..41306610,3	MCF-7	breast:
11	chr17:21187580..21188318-chr19:41304839..41305614,2	HCT-116	colon:
12	chr19:41220369..41226479-chr19:41305318..41310706,7	K562	blood:
13	chr19:41253776..41259894-chr19:41301950..41310086,19	MCF-7	breast:
14	chr19:41220238..41223312-chr19:41303618..41307521,4	K562	blood:
15	chr19:41283422..41285801-chr19:41305183..41308009,2	MCF-7	breast:
16	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:
17	chr19:41220057..41225402-chr19:41302090..41307926,9	MCF-7	breast:
18	chr19:41223981..41226562-chr19:41304181..41307698,5	MCF-7	breast:

Variant related genes	Relation type
EGLN2	TF binding region
ENSG00000268797	TF binding region
ENSG00000086544	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000034152	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000086061	Chromatin interaction
ENSG00000137074	Chromatin interaction
ENSG00000256612	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000167578	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs45600135	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4802088	1.00[MEX][hapmap]
rs4803365	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4803367	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4803370	0.85[EUR][1000 genomes]
rs7251781	0.95[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	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34406232	CNTNAP2	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41303400-41306200	Active TSS	Thymus	Thymus
2	chr19:41303800-41305800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:41303800-41306000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr19:41303800-41306200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:41303800-41306200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr19:41303800-41306400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr19:41303800-41306400	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr19:41303800-41306600	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr19:41304000-41306000	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr19:41304000-41306000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:41304000-41306000	Active TSS	Gastric	stomach
12	chr19:41304000-41306000	Active TSS	Right Atrium	heart
13	chr19:41304000-41306200	Active TSS	Aorta	Aorta
14	chr19:41304000-41306200	Active TSS	Ovary	ovary
15	chr19:41304000-41306400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr19:41304000-41306400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr19:41304000-41306400	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr19:41304000-41306400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr19:41304000-41306400	Active TSS	Fetal Kidney	kidney
20	chr19:41304000-41306400	Active TSS	HSMMtube	muscle
21	chr19:41304000-41306800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr19:41304200-41305800	Active TSS	Pancreas	Pancrea
23	chr19:41304200-41306000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr19:41304200-41306000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr19:41304200-41306000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:41304200-41306000	Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr19:41304200-41306000	Active TSS	Brain Angular Gyrus	brain
28	chr19:41304200-41306000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:41304200-41306000	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr19:41304200-41306000	Active TSS	Right Ventricle	heart
31	chr19:41304200-41306000	Active TSS	Stomach Mucosa	stomach
32	chr19:41304200-41306200	Active TSS	H1 Cell Line	embryonic stem cell
33	chr19:41304200-41306200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:41304200-41306200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:41304200-41306200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:41304200-41306200	Active TSS	Brain Anterior Caudate	brain
37	chr19:41304200-41306200	Active TSS	Esophagus	oesophagus
38	chr19:41304200-41306200	Active TSS	Left Ventricle	heart
39	chr19:41304200-41306200	Active TSS	Lung	lung
40	chr19:41304200-41306200	Active TSS	Placenta Amnion	Placenta Amnion
41	chr19:41304200-41306400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr19:41304200-41306400	Active TSS	Colon Smooth Muscle	Colon
43	chr19:41304200-41306400	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr19:41304200-41306600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:41304200-41306600	Active TSS	Psoas Muscle	Psoas
46	chr19:41304200-41306600	Active TSS	NHDF-Ad	bronchial
47	chr19:41304400-41305600	Active TSS	Primary B cells from cord blood	blood
48	chr19:41304400-41305600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr19:41304400-41305600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr19:41304400-41305600	Active TSS	Stomach Smooth Muscle	stomach

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