Variant report

Variant	rs3826994
Chromosome Location	chr19:19245511-19245512
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	TBP	chr19:19245446-19246146	K562	blood:	n/a	n/a
2	CBX3	chr19:19245408-19246090	K562	blood:	n/a	n/a
3	JUND	chr19:19245467-19245958	H1-hESC	embryonic stem cell:	n/a	n/a
4	CHD2	chr19:19245511-19245992	K562	blood:	n/a	chr19:19245699-19245709
5	SP1	chr19:19245306-19246085	H1-hESC	embryonic stem cell:	n/a	chr19:19245526-19245536 chr19:19245700-19245709 chr19:19245578-19245587 chr19:19245564-19245578 chr19:19245563-19245575 chr19:19245577-19245589 chr19:19245564-19245574 chr19:19245522-19245531 chr19:19245873-19245887 chr19:19245699-19245711 chr19:19245579-19245588 chr19:19245791-19245805 chr19:19245563-19245575 chr19:19245579-19245588 chr19:19245699-19245710 chr19:19245577-19245589
6	POLR2A	chr19:19245461-19246194	K562	blood:	n/a	n/a
7	POLR2A	chr19:19245461-19246136	K562	blood:	n/a	n/a
8	ZEB1	chr19:19245481-19245786	GM12878	blood:	n/a	chr19:19245586-19245595
9	TAF1	chr19:19245470-19245939	H1-hESC	embryonic stem cell:	n/a	n/a
10	NR2F2	chr19:19245445-19246024	K562	blood:	n/a	n/a
11	JUND	chr19:19245456-19246034	K562	blood:	n/a	n/a
12	MAZ	chr19:19245409-19246092	K562	blood:	n/a	chr19:19245564-19245574 chr19:19245954-19245964
13	POLR2A	chr19:19245445-19245869	H1-hESC	embryonic stem cell:	n/a	n/a
14	PML	chr19:19245383-19245923	K562	blood:	n/a	n/a
15	POLR2A	chr19:19245466-19246243	K562	blood:	n/a	n/a
16	MAX	chr19:19245455-19246009	K562	blood:	n/a	chr19:19245564-19245574 chr19:19245954-19245964
17	MAX	chr19:19245421-19246275	K562	blood:	n/a	chr19:19245564-19245574 chr19:19245954-19245964
18	EGR1	chr19:19245403-19246102	K562	blood:	n/a	chr19:19245958-19245969
19	MYC	chr19:19245500-19246081	K562	blood:	n/a	chr19:19245564-19245574 chr19:19245954-19245964
20	HDAC2	chr19:19245475-19245788	K562	blood:	n/a	n/a
21	CCNT2	chr19:19245453-19245892	K562	blood:	n/a	chr19:19245700-19245709
22	USF1	chr19:19245415-19245935	K562	blood:	n/a	chr19:19245720-19245736
23	CTCF	chr19:19245500-19245650	HCT-116	colon:	n/a	chr19:19245538-19245554 chr19:19245537-19245555
24	BHLHE40	chr19:19245504-19246217	K562	blood:	n/a	chr19:19245720-19245736
25	POLR2A	chr19:19245317-19246345	K562	blood:	n/a	n/a
26	SP4	chr19:19245339-19245991	H1-hESC	embryonic stem cell:	n/a	chr19:19245541-19245557 chr19:19245699-19245710
27	ELF1	chr19:19245460-19245736	K562	blood:	n/a	n/a
28	POLR2A	chr19:19245330-19245884	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr19:19245492-19245718	K562	blood:	n/a	chr19:19245538-19245554 chr19:19245537-19245555
30	TEAD4	chr19:19245407-19246078	K562	blood:	n/a	n/a
31	POLR2A	chr19:19245508-19245773	H1-hESC	embryonic stem cell:	n/a	n/a
32	TAF1	chr19:19245480-19245831	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr19:19245493-19246124	K562	blood:	n/a	chr19:19245538-19245554 chr19:19245537-19245555
34	TBP	chr19:19245492-19245824	H1-hESC	embryonic stem cell:	n/a	n/a
35	CREB1	chr19:19245415-19246121	H1-hESC	embryonic stem cell:	n/a	n/a
36	TAF1	chr19:19245472-19245900	K562	blood:	n/a	n/a
37	POLR2A	chr19:19245456-19245772	HCT-116	colon:	n/a	n/a
38	MXI1	chr19:19245488-19245919	K562	blood:	n/a	n/a
39	JUN	chr19:19245302-19245978	K562	blood:	n/a	n/a
40	HEY1	chr19:19245503-19246011	K562	blood:	n/a	n/a
41	POLR2A	chr19:19245456-19245994	K562	blood:	n/a	n/a
42	SP4	chr19:19245342-19246006	H1-hESC	embryonic stem cell:	n/a	chr19:19245541-19245557 chr19:19245699-19245710
43	YY1	chr19:19245508-19245979	K562	blood:	n/a	n/a
44	RCOR1	chr19:19245506-19246197	K562	blood:	n/a	n/a
45	TAF1	chr19:19245499-19245742	K562	blood:	n/a	n/a
46	E2F6	chr19:19245408-19245805	K562	blood:	n/a	n/a
47	IRF1	chr19:19245361-19246002	K562	blood:	n/a	chr19:19245545-19245559 chr19:19245577-19245591
48	YY1	chr19:19245403-19246053	K562	blood:	n/a	n/a
49	NR2F2	chr19:19245409-19246532	K562	blood:	n/a	n/a
50	MEF2A	chr19:19245481-19246034	K562	blood:	n/a	chr19:19245765-19245780 chr19:19245765-19245781 chr19:19245766-19245781 chr19:19245766-19245780 chr19:19245764-19245785 chr19:19245769-19245778 chr19:19245764-19245785 chr19:19245767-19245778 chr19:19245764-19245785 chr19:19245768-19245779

No.	Distal block	Cell Line	Cell type
1	chr19:19229745..19232931-chr19:19245473..19249545,7	K562	blood:
2	chr19:19162153..19163903-chr19:19245411..19247437,2	K562	blood:
3	chr19:19143649..19145293-chr19:19243998..19245856,2	MCF-7	breast:
4	chr19:19143484..19146090-chr19:19245297..19247297,2	K562	blood:
5	chr19:19165962..19168067-chr19:19244152..19247081,2	K562	blood:
6	chr19:19214932..19216511-chr19:19243941..19245659,2	K562	blood:
7	chr19:19244353..19247237-chr19:19256209..19258577,3	K562	blood:
8	chr19:19241159..19242979-chr19:19243469..19246036,2	K562	blood:
9	chr19:19229446..19234006-chr19:19241302..19251526,15	K562	blood:
10	chr19:19169646..19176667-chr19:19241603..19249514,19	K562	blood:
11	chr19:19244048..19247322-chr19:19247379..19249881,3	MCF-7	breast:
12	chr19:19169646..19176603-chr19:19241603..19250623,23	K562	blood:
13	chr19:19243871..19246499-chr19:19246795..19249258,3	MCF-7	breast:

Variant related genes	Relation type
TMEM161A	TF binding region
ENSG00000105676	Chromatin interaction
ENSG00000064607	Chromatin interaction
ENSG00000181035	Chromatin interaction
ENSG00000064545	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs16995885	0.83[JPT][hapmap]
rs3826993	0.90[CHB][hapmap]
rs964132	0.94[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3826994	ZNF429	cis	parietal	SCAN
rs3826994	CPAMD8	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19180600-19245600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:19180600-19248400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:19203800-19245600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr19:19217200-19247800	Weak transcription	Right Atrium	heart
5	chr19:19220400-19247800	Weak transcription	Psoas Muscle	Psoas
6	chr19:19222200-19248200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr19:19230800-19248400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr19:19231200-19248000	Weak transcription	Fetal Brain Male	brain
9	chr19:19231800-19245600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:19232600-19248000	Weak transcription	NHLF	lung
11	chr19:19233200-19245600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr19:19234600-19248000	Weak transcription	Primary B cells from cord blood	blood
13	chr19:19234800-19247800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:19235000-19247800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:19235200-19245600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr19:19243200-19245600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr19:19243200-19248000	Weak transcription	Osteobl	bone
18	chr19:19243400-19245600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr19:19243400-19245600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr19:19243400-19247800	Weak transcription	Right Ventricle	heart
21	chr19:19243400-19247800	Weak transcription	Stomach Mucosa	stomach
22	chr19:19243400-19248200	Weak transcription	Fetal Brain Female	brain
23	chr19:19243400-19248200	Weak transcription	Fetal Lung	lung
24	chr19:19243600-19245600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr19:19243600-19245600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:19243600-19245600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:19243600-19245600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr19:19243600-19245600	Weak transcription	Brain Germinal Matrix	brain
29	chr19:19243600-19245600	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:19243600-19245600	Weak transcription	Ovary	ovary
31	chr19:19243600-19247800	Weak transcription	Liver	Liver
32	chr19:19243600-19247800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr19:19243600-19248000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:19243600-19248000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:19243600-19248000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr19:19243600-19248000	Weak transcription	Colon Smooth Muscle	Colon
37	chr19:19243600-19248000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr19:19243600-19248200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr19:19243600-19248200	Weak transcription	Colonic Mucosa	Colon
40	chr19:19243600-19248400	Weak transcription	Brain Substantia Nigra	brain
41	chr19:19243600-19248400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr19:19243600-19248400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr19:19243800-19245600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:19243800-19245600	Weak transcription	Esophagus	oesophagus
45	chr19:19243800-19245600	Weak transcription	Pancreas	Pancrea
46	chr19:19243800-19245800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr19:19243800-19247600	Weak transcription	HepG2	liver
48	chr19:19243800-19247800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr19:19243800-19247800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:19243800-19247800	Weak transcription	Adipose Nuclei	Adipose

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