Variant report

Variant	rs413901
Chromosome Location	chr19:41090260-41090261
allele	C/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	chr19:41089985-41090306	K562	blood:	n/a	chr19:41090138-41090147
2	SP1	chr19:41089864-41090474	A549	lung:	n/a	n/a
3	FOXA2	chr19:41089800-41090423	A549	lung:	n/a	n/a
4	CTCF	chr19:41090140-41090290	GM06990	blood:	n/a	n/a
5	FOXA2	chr19:41089777-41090389	A549	lung:	n/a	n/a
6	CTCF	chr19:41090140-41090290	GM12870	blood:	n/a	n/a
7	CTCF	chr19:41089985-41090342	HCT-116	colon:	n/a	chr19:41090138-41090147
8	FOS	chr19:41089968-41090266	MCF10A-Er-Src	breast:	n/a	n/a
9	CTCF	chr19:41090120-41090270	SAEC	small airway:	n/a	chr19:41090138-41090147
10	FOS	chr19:41089898-41090301	MCF10A-Er-Src	breast:	n/a	n/a
11	CTCF	chr19:41090240-41090390	A549	lung:	n/a	n/a
12	MYC	chr19:41089813-41090858	A549	lung:	n/a	n/a
13	CTCF	chr19:41090120-41090270	BJ	skin:	n/a	chr19:41090138-41090147
14	CTCF	chr19:41089959-41090312	A549	lung:	n/a	chr19:41090138-41090147
15	CTCF	chr19:41090002-41090290	K562	blood:	n/a	chr19:41090138-41090147
16	MAX	chr19:41089956-41090373	A549	lung:	n/a	n/a
17	RAD21	chr19:41089995-41090349	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr19:41090120-41090270	GM12872	blood:	n/a	chr19:41090138-41090147
19	CTCF	chr19:41089973-41090300	K562	blood:	n/a	chr19:41090138-41090147
20	CTCF	chr19:41090120-41090270	HRE	kidney:	n/a	chr19:41090138-41090147
21	CTCF	chr19:41090200-41090350	HMEC	breast:	n/a	n/a
22	CTCF	chr19:41089972-41090403	A549	lung:	n/a	chr19:41090138-41090147
23	CTCF	chr19:41090120-41090270	RPTEC	kidney:	n/a	chr19:41090138-41090147
24	CTCF	chr19:41090160-41090310	GM12878	blood:	n/a	n/a
25	CTCF	chr19:41090120-41090270	HCM	heart:	n/a	chr19:41090138-41090147
26	CTCF	chr19:41090018-41090283	IMR90	lung:	n/a	chr19:41090138-41090147
27	CTCF	chr19:41090180-41090330	NHDF-neo	bronchial:	n/a	n/a
28	CTCF	chr19:41090120-41090270	HUVEC	blood vessel:	n/a	chr19:41090138-41090147
29	MAX	chr19:41090026-41090333	A549	lung:	n/a	n/a
30	RAD21	chr19:41090010-41090404	A549	lung:	n/a	n/a
31	CTCF	chr19:41090120-41090270	GM12871	blood:	n/a	chr19:41090138-41090147
32	RAD21	chr19:41089950-41090487	A549	lung:	n/a	n/a
33	FOSL2	chr19:41089791-41090453	A549	lung:	n/a	n/a
34	CTCF	chr19:41090200-41090350	NHEK	skin:	n/a	n/a
35	CTCF	chr19:41089991-41090282	A549	lung:	n/a	chr19:41090138-41090147
36	MAX	chr19:41089942-41090541	A549	lung:	n/a	n/a
37	CTCF	chr19:41089788-41091199	A549	lung:	n/a	chr19:41090138-41090147
38	FOSL2	chr19:41089932-41090265	A549	lung:	n/a	n/a
39	CTCF	chr19:41090120-41090270	GM12801	blood:	n/a	chr19:41090138-41090147
40	RAD21	chr19:41090029-41090288	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr19:41090028-41090270	K562	blood:	n/a	chr19:41090138-41090147
42	RAD21	chr19:41090008-41090323	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41088760..41090446-chr19:41117467..41120079,2	K562	blood:
2	chr19:41087979..41091275-chr19:41098562..41102111,3	MCF-7	breast:
3	chr19:41089392..41091268-chr19:41092459..41096170,3	K562	blood:
4	chr19:41082792..41084497-chr19:41089629..41092124,2	MCF-7	breast:
5	chr19:41089607..41091803-chr19:41093435..41095307,2	MCF-7	breast:
6	chr19:41089494..41092756-chr19:41107049..41110047,4	K562	blood:

Variant related genes	Relation type
SHKBP1	TF binding region
ENSG00000160410	Chromatin interaction
ENSG00000090006	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10402698	0.92[ASN][1000 genomes]
rs10403963	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs10405930	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs10410606	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs1051303	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs11083560	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs1131620	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs1864074	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs1864078	0.83[CHB][hapmap]
rs2303729	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs2369006	0.83[CHB][hapmap]
rs2604902	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs392726	0.89[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs393569	0.89[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs396118	0.87[ASN][1000 genomes]
rs404584	0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs406133	0.90[ASN][1000 genomes]
rs410101	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs415075	0.91[ASN][1000 genomes]
rs420490	0.83[ASN][1000 genomes]
rs420720	0.88[ASN][1000 genomes]
rs421739	0.81[CEU][hapmap]
rs710160	0.81[CEU][hapmap]
rs7171	0.88[ASN][1000 genomes]
rs7259067	0.85[CHD][hapmap]
rs7259237	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs7259554	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs8107014	0.83[CHB][hapmap];0.83[CHD][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs413901	B9D2	cis	parietal	SCAN
rs413901	ZNF296	cis	cerebellum	SCAN
rs413901	CEACAM6	cis	cerebellum	SCAN
rs413901	KCNN4	cis	cerebellum	SCAN
rs413901	PGLYRP1	cis	cerebellum	SCAN
rs413901	DMRTC2	cis	cerebellum	SCAN
rs413901	LTBP4	cis	multi-tissue	Pritchard
rs413901	CA11	cis	cerebellum	SCAN
rs413901	QPCTL	cis	cerebellum	SCAN
rs413901	GEMIN7	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41083600-41091200	Weak transcription	Psoas Muscle	Psoas
2	chr19:41083600-41092800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:41083600-41093600	Weak transcription	Fetal Lung	lung
4	chr19:41083600-41095400	Weak transcription	Fetal Kidney	kidney
5	chr19:41083600-41100400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:41083600-41101000	Weak transcription	HSMMtube	muscle
7	chr19:41084000-41091600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:41084000-41094000	Weak transcription	HSMM	muscle
9	chr19:41084000-41095400	Strong transcription	Fetal Intestine Small	intestine
10	chr19:41084000-41097600	Strong transcription	Fetal Stomach	stomach
11	chr19:41084200-41091200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr19:41084200-41093800	Weak transcription	NHEK	skin
13	chr19:41084200-41099800	Weak transcription	Fetal Brain Male	brain
14	chr19:41084400-41090800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:41084400-41091600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:41084400-41092000	Weak transcription	HepG2	liver
17	chr19:41084400-41094200	Weak transcription	HMEC	breast
18	chr19:41084400-41100000	Weak transcription	Stomach Mucosa	stomach
19	chr19:41084600-41091000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:41084600-41095200	Strong transcription	Fetal Muscle Leg	muscle
21	chr19:41084600-41097600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr19:41084600-41100400	Weak transcription	NHDF-Ad	bronchial
23	chr19:41084600-41102600	Weak transcription	Right Atrium	heart
24	chr19:41084800-41096600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr19:41084800-41097200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr19:41084800-41097600	Strong transcription	Thymus	Thymus
27	chr19:41085000-41091000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr19:41085200-41090800	Strong transcription	Placenta	Placenta
29	chr19:41085200-41094000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:41085400-41090600	Strong transcription	Osteobl	bone
31	chr19:41085400-41094800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:41085400-41097200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr19:41085600-41091600	Strong transcription	Fetal Thymus	thymus
34	chr19:41085800-41090600	Strong transcription	Dnd41	blood
35	chr19:41085800-41090600	Strong transcription	NHLF	lung
36	chr19:41085800-41090800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:41085800-41095200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:41085800-41095200	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr19:41086000-41090400	Strong transcription	Liver	Liver
40	chr19:41086000-41090600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr19:41086000-41090600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr19:41086000-41090600	Strong transcription	Rectal Smooth Muscle	rectum
43	chr19:41086000-41090800	Strong transcription	Adipose Nuclei	Adipose
44	chr19:41086000-41090800	Strong transcription	Lung	lung
45	chr19:41086000-41091200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:41086000-41094600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr19:41086000-41094800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:41086000-41095200	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr19:41086000-41095200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr19:41086000-41097200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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