Variant report

Variant	rs3786527
Chromosome Location	chr19:41109456-41109457
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	CTCF	chr19:41109320-41109470	A549	lung:	n/a	n/a
2	CTCF	chr19:41109299-41109459	GM12878	blood:	n/a	n/a
3	MAZ	chr19:41109350-41110385	Hela-S3	cervix:	n/a	chr19:41109621-41109631 chr19:41110033-41110043 chr19:41109693-41109703 chr19:41110085-41110095
4	FOSL2	chr19:41107922-41112397	A549	lung:	n/a	chr19:41110415-41110427
5	MAX	chr19:41109057-41112684	A549	lung:	n/a	chr19:41109621-41109631 chr19:41110033-41110043 chr19:41112230-41112240 chr19:41109693-41109703 chr19:41110085-41110095
6	CTCF	chr19:41109254-41109537	IMR90	lung:	n/a	n/a
7	TEAD4	chr19:41109437-41110529	ECC-1	luminal epithelium:	n/a	n/a
8	CTCF	chr19:41109340-41109490	K562	blood:	n/a	n/a
9	HNF4G	chr19:41109450-41110089	HepG2	liver:	n/a	chr19:41109733-41109745 chr19:41109733-41109745
10	CTCF	chr19:41109320-41109470	AG09309	skin:	n/a	n/a
11	CTCF	chr19:41109400-41109550	HRE	kidney:	n/a	n/a
12	POLR2A	chr19:41109149-41112024	K562	blood:	n/a	n/a
13	UBTF	chr19:41109326-41109868	K562	blood:	n/a	n/a
14	MAZ	chr19:41109142-41110302	HepG2	liver:	n/a	chr19:41109621-41109631 chr19:41110033-41110043 chr19:41109693-41109703 chr19:41110085-41110095
15	CCNT2	chr19:41109345-41110133	K562	blood:	n/a	n/a
16	POLR2A	chr19:41109071-41110034	K562	blood:	n/a	n/a
17	GTF2F1	chr19:41109267-41110132	Hela-S3	cervix:	n/a	n/a
18	EP300	chr19:41109453-41110086	HepG2	liver:	n/a	n/a
19	CTCF	chr19:41107334-41112542	A549	lung:	n/a	chr19:41110180-41110196 chr19:41108676-41108684 chr19:41108186-41108199 chr19:41108187-41108196 chr19:41110184-41110194 chr19:41108671-41108689 chr19:41108181-41108199 chr19:41108183-41108196 chr19:41108666-41108687 chr19:41108184-41108194
20	ZBTB7A	chr19:41109410-41110422	ECC-1	luminal epithelium:	n/a	n/a
21	CTCF	chr19:41109261-41109582	MCF-7	breast:	n/a	n/a
22	TCF12	chr19:41107775-41112752	A549	lung:	n/a	chr19:41110897-41110905 chr19:41109793-41109800 chr19:41111228-41111238 chr19:41109824-41109831
23	CTCF	chr19:41109320-41109470	RPTEC	kidney:	n/a	n/a
24	TCF12	chr19:41109419-41110734	ECC-1	luminal epithelium:	n/a	chr19:41109793-41109800 chr19:41109824-41109831
25	MAX	chr19:41109409-41110576	ECC-1	luminal epithelium:	n/a	chr19:41109621-41109631 chr19:41110033-41110043 chr19:41109693-41109703 chr19:41110085-41110095
26	TCF12	chr19:41109114-41110470	A549	lung:	n/a	chr19:41109793-41109800 chr19:41109824-41109831
27	ZNF143	chr19:41109190-41109748	K562	blood:	n/a	n/a
28	BHLHE40	chr19:41109373-41109905	K562	blood:	n/a	n/a
29	CUX1	chr19:41109197-41109714	K562	blood:	n/a	n/a
30	MYBL2	chr19:41109455-41110152	HepG2	liver:	n/a	n/a
31	TCF7L2	chr19:41109434-41110438	HCT-116	colon:	n/a	chr19:41109489-41109498
32	HDAC2	chr19:41109215-41109755	K562	blood:	n/a	n/a
33	CTCF	chr19:41109320-41109470	HMF	breast:	n/a	n/a
34	EP300	chr19:41109279-41110228	K562	blood:	n/a	n/a
35	FOSL2	chr19:41109355-41110501	A549	lung:	n/a	chr19:41110415-41110427
36	CTCF	chr19:41109320-41109470	NHDF-neo	bronchial:	n/a	n/a
37	IRF1	chr19:41109035-41109589	K562	blood:	n/a	n/a
38	KAP1	chr19:41109278-41110116	U2OS	brain:	n/a	n/a
39	REST	chr19:41109149-41109742	K562	blood:	n/a	n/a
40	CTCF	chr19:41109142-41109548	A549	lung:	n/a	n/a
41	FOXA2	chr19:41109395-41110560	A549	lung:	n/a	n/a
42	CTCF	chr19:41109320-41109470	HRE	kidney:	n/a	n/a
43	CTCF	chr19:41109227-41109517	K562	blood:	n/a	n/a
44	JUND	chr19:41109085-41110196	K562	blood:	n/a	n/a
45	EP300	chr19:41109414-41109980	HepG2	liver:	n/a	n/a
46	REST	chr19:41109168-41109538	H1-hESC	embryonic stem cell:	n/a	n/a
47	REST	chr19:41107638-41112355	A549	lung:	n/a	chr19:41109783-41109796 chr19:41110030-41110043 chr19:41111216-41111224 chr19:41108709-41108719 chr19:41112104-41112117 chr19:41112227-41112240 chr19:41108218-41108231
48	SIN3AK20	chr19:41108846-41112253	A549	lung:	n/a	n/a
49	TBL1XR1	chr19:41109299-41109597	K562	blood:	n/a	n/a
50	CTCF	chr19:41109342-41109458	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41033096..41035483-chr19:41108426..41110262,2	MCF-7	breast:
2	chr19:41109313..41109956-chr19:41168644..41169356,2	K562	blood:
3	chr19:41030467..41033307-chr19:41108722..41110398,2	MCF-7	breast:
4	chr19:40909995..40911526-chr19:41108177..41110853,2	K562	blood:
5	chr19:40967363..40973578-chr19:41101518..41109514,8	K562	blood:
6	chr19:41109242..41109896-chr19:41140100..41140769,2	MCF-7	breast:
7	chr19:40969243..40970765-chr19:41108513..41110039,2	MCF-7	breast:
8	chr19:41053869..41056282-chr19:41108308..41111059,2	MCF-7	breast:
9	chr19:41107019..41113650-chr19:41128672..41134191,9	K562	blood:
10	chr19:40931237..40933267-chr19:41108598..41112233,4	K562	blood:
11	chr19:41075066..41076899-chr19:41107772..41111753,3	K562	blood:
12	chr19:41035178..41037459-chr19:41108558..41111461,2	MCF-7	breast:
13	chr19:41081216..41084507-chr19:41109456..41112097,3	MCF-7	breast:
14	chr19:41108472..41109833-chr19:41140193..41141071,7	MCF-7	breast:
15	chr19:41031800..41040224-chr19:41101608..41111828,17	K562	blood:
16	chr19:40949457..40951566-chr19:41109305..41111176,2	K562	blood:
17	chr19:41084714..41088277-chr19:41106890..41109795,3	K562	blood:
18	chr19:41031800..41041078-chr19:41106134..41114466,15	K562	blood:
19	chr19:41074602..41077015-chr19:41107246..41111753,6	K562	blood:
20	chr19:41108422..41113817-chr19:41128876..41134100,7	MCF-7	breast:
21	chr19:40970640..40973195-chr19:41107920..41111386,3	K562	blood:
22	chr19:41109366..41111519-chr19:41767737..41769889,2	MCF-7	breast:
23	chr19:41089494..41092756-chr19:41107049..41110047,4	K562	blood:
24	chr19:41107627..41110532-chr19:41140107..41142181,2	K562	blood:
25	chr19:41084483..41086767-chr19:41108737..41110541,2	MCF-7	breast:
26	chr19:40927815..40929486-chr19:41109339..41111164,2	K562	blood:
27	chr19:41108549..41110281-chr19:41195453..41197402,2	MCF-7	breast:
28	chr19:41108277..41110183-chr19:41222910..41224615,2	MCF-7	breast:

Variant related genes	Relation type
LTBP4	TF binding region
ENSG00000167565	Chromatin interaction
ENSG00000090013	Chromatin interaction
ENSG00000160410	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000160460	Chromatin interaction
ENSG00000197019	Chromatin interaction
ENSG00000123815	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10403963	0.80[JPT][hapmap]
rs1051303	0.80[JPT][hapmap]
rs11083560	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs2246761	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303728	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802079	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55740667	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55815263	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62107907	0.92[ASN][1000 genomes]
rs62107911	0.91[ASN][1000 genomes]
rs62107913	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62107917	0.81[EUR][1000 genomes]
rs7259237	0.80[JPT][hapmap]
rs7259554	0.80[JPT][hapmap]
rs73047963	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73047967	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107014	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911714	chr19:41006426-41165252	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv911715	chr19:41014922-41141434	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1057634	chr19:41019512-41174259	Enhancers Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv911716	chr19:41023511-41109456	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv911717	chr19:41023511-41141434	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv911719	chr19:41033109-41147087	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911720	chr19:41033109-41156940	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv911721	chr19:41040334-41124931	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv911722	chr19:41040334-41176403	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv869561	chr19:41077513-41139834	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv1064699	chr19:41086506-41174259	Genic enhancers Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
14	nsv911724	chr19:41089505-41165252	Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
15	nsv911725	chr19:41090190-41114065	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	nsv911726	chr19:41090190-41141434	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3786527	PGLYRP1	cis	cerebellum	SCAN
rs3786527	PRR19	cis	cerebellum	SCAN
rs3786527	CA11	cis	cerebellum	SCAN
rs3786527	KDELR1	cis	cerebellum	SCAN
rs3786527	ELSPBP1	cis	cerebellum	SCAN
rs3786527	IRGQ	cis	cerebellum	SCAN
rs3786527	KCNN4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41106000-41136800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:41106400-41109800	Active TSS	Aorta	Aorta
3	chr19:41107200-41110000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:41107400-41109600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr19:41107400-41109600	Bivalent Enhancer	Fetal Thymus	thymus
6	chr19:41107400-41110200	Flanking Active TSS	NHLF	lung
7	chr19:41107400-41110400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
8	chr19:41107600-41109600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:41107600-41109600	Flanking Active TSS	Fetal Intestine Large	intestine
10	chr19:41107600-41109600	Enhancers	Pancreas	Pancrea
11	chr19:41107800-41109600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr19:41107800-41109600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:41107800-41109600	Enhancers	Brain Substantia Nigra	brain
14	chr19:41107800-41109600	Flanking Active TSS	Fetal Lung	lung
15	chr19:41107800-41109600	Flanking Active TSS	A549	lung
16	chr19:41108000-41109600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:41108000-41109600	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr19:41108000-41109600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:41108000-41109600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:41108000-41109600	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr19:41108000-41109600	Flanking Active TSS	NHEK	skin
22	chr19:41108000-41110400	Flanking Active TSS	Fetal Intestine Small	intestine
23	chr19:41108000-41110600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:41108200-41109600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
25	chr19:41108200-41109600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:41108200-41109600	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr19:41108200-41109600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr19:41108200-41109800	Flanking Active TSS	Colonic Mucosa	Colon
29	chr19:41108200-41109800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
30	chr19:41108200-41111000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:41108400-41109600	Flanking Active TSS	K562	blood
32	chr19:41108600-41109600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:41108600-41109600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:41108600-41109600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr19:41108600-41109600	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr19:41108600-41109600	Flanking Active TSS	Hela-S3	cervix
37	chr19:41108600-41109600	Flanking Active TSS	NHDF-Ad	bronchial
38	chr19:41108800-41109600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr19:41108800-41109600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:41108800-41109600	Enhancers	Esophagus	oesophagus
41	chr19:41108800-41109600	Flanking Active TSS	Fetal Kidney	kidney
42	chr19:41108800-41109600	Flanking Active TSS	Fetal Stomach	stomach
43	chr19:41108800-41109600	Flanking Active TSS	HSMMtube	muscle
44	chr19:41108800-41110200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr19:41108800-41110800	Enhancers	Primary T cells from cord blood	blood
46	chr19:41108800-41111000	Enhancers	Liver	Liver
47	chr19:41108800-41111600	Enhancers	Stomach Mucosa	stomach
48	chr19:41109000-41109600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
49	chr19:41109000-41109600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
50	chr19:41109000-41109800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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