Variant report

Variant	rs10405930
Chromosome Location	chr19:41116866-41116867
allele	C/T
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	chr19:41114826-41117365	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:41114946-41117153	MCF10A-Er-Src	breast:	n/a	n/a
3	ZNF263	chr19:41116760-41118334	HEK293-T-REx	kidney:	n/a	chr19:41117469-41117490 chr19:41117480-41117489 chr19:41117907-41117916
4	MAFK	chr19:41116587-41116931	HepG2	liver:	n/a	chr19:41116759-41116769 chr19:41116920-41116930
5	POLR2A	chr19:41114805-41117539	K562	blood:	n/a	n/a
6	MAFK	chr19:41116719-41116892	IMR90	lung:	n/a	chr19:41116759-41116769
7	POLR2A	chr19:41115253-41117026	SK-N-MC	brain:	n/a	n/a
8	MAFK	chr19:41116624-41116900	HepG2	liver:	n/a	chr19:41116759-41116769
9	MAFK	chr19:41116675-41116909	Hela-S3	cervix:	n/a	chr19:41116759-41116769
10	POLR2A	chr19:41116853-41117040	H1-hESC	embryonic stem cell:	n/a	n/a
11	RCOR1	chr19:41116702-41116902	K562	blood:	n/a	n/a
12	POLR2A	chr19:41114965-41117433	Hela-S3	cervix:	n/a	n/a
13	MAFF	chr19:41116669-41116916	HepG2	liver:	n/a	n/a
14	BACH1	chr19:41116648-41116931	H1-hESC	embryonic stem cell:	n/a	chr19:41116758-41116772
15	POLR2A	chr19:41114887-41117244	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40930916..40933044-chr19:41115894..41119159,3	MCF-7	breast:
2	chr19:41093158..41095920-chr19:41115359..41117293,2	K562	blood:
3	chr19:40929828..40933213-chr19:41114237..41116915,3	MCF-7	breast:
4	chr19:41115624..41118176-chr19:41306706..41309360,2	MCF-7	breast:
5	chr19:41081088..41083004-chr19:41115582..41117218,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL758P	TF binding region
LTBP4	TF binding region
ENSG00000268797	Chromatin interaction
ENSG00000197019	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000160410	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10402698	0.80[ASN][1000 genomes]
rs10403467	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10403833	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10403963	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10410606	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1051303	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083561	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1131620	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11667706	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11667772	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11668582	0.87[EUR][1000 genomes]
rs12610819	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs12611045	0.96[ASN][1000 genomes]
rs12980111	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1318544	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864074	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1864078	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1869712	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278242	0.83[CHB][hapmap]
rs2278246	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303727	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303729	0.87[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2369006	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2604902	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28571670	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28649715	0.96[ASN][1000 genomes]
rs28655571	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs392726	0.94[CHB][hapmap];0.93[CHD][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs393569	0.94[CHB][hapmap];0.85[CHD][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs396118	0.87[ASN][1000 genomes]
rs404584	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs406133	0.83[ASN][1000 genomes]
rs410101	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs413901	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs415075	0.84[ASN][1000 genomes]
rs420720	0.86[ASN][1000 genomes]
rs4803348	0.96[ASN][1000 genomes]
rs56353506	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7171	0.88[ASN][1000 genomes]
rs7257696	0.81[CHD][hapmap]
rs7259067	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7259237	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7259554	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107014	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs919307	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
16	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
17	nsv870022	chr19:41113071-41178982	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10405930	PGLYRP1	cis	cerebellum	SCAN
rs10405930	B9D2	cis	parietal	SCAN
rs10405930	QPCTL	cis	cerebellum	SCAN
rs10405930	CEACAM6	cis	cerebellum	SCAN
rs10405930	ZNF296	cis	cerebellum	SCAN
rs10405930	CA11	cis	cerebellum	SCAN

Chromatin state (count:104 , 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	chr19:41109800-41122600	Weak transcription	Aorta	Aorta
3	chr19:41110000-41118200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:41114400-41119400	Weak transcription	Ovary	ovary
5	chr19:41114800-41117400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr19:41115000-41118000	Weak transcription	Fetal Kidney	kidney
7	chr19:41115200-41117000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr19:41115200-41117400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:41115200-41117800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
10	chr19:41115200-41118000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:41115200-41118000	Flanking Active TSS	HMEC	breast
12	chr19:41115400-41117000	Bivalent Enhancer	Fetal Heart	heart
13	chr19:41115400-41117000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr19:41115800-41117000	Enhancers	Primary T cells from cord blood	blood
15	chr19:41115800-41117000	Enhancers	Lung	lung
16	chr19:41115800-41118200	Enhancers	Spleen	Spleen
17	chr19:41116000-41117000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:41116000-41117000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr19:41116000-41117200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:41116000-41117400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr19:41116000-41118000	Flanking Active TSS	NHEK	skin
22	chr19:41116200-41117000	Enhancers	Primary B cells from cord blood	blood
23	chr19:41116200-41117000	Genic enhancers	Fetal Lung	lung
24	chr19:41116200-41117000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr19:41116200-41117200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:41116200-41117200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr19:41116200-41117200	Active TSS	HSMMtube	muscle
28	chr19:41116200-41117400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr19:41116200-41117400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:41116200-41117400	Flanking Active TSS	Colonic Mucosa	Colon
31	chr19:41116200-41117600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:41116200-41118000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr19:41116400-41117000	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr19:41116400-41117000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr19:41116400-41117000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr19:41116400-41117000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:41116400-41117000	Enhancers	Pancreas	Pancrea
38	chr19:41116400-41117000	Enhancers	HUVEC	blood vessel
39	chr19:41116400-41117000	Enhancers	K562	blood
40	chr19:41116400-41117200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
41	chr19:41116400-41117200	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr19:41116400-41117200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr19:41116400-41117400	Enhancers	Gastric	stomach
44	chr19:41116400-41117600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:41116400-41117800	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr19:41116400-41119000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:41116400-41119200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:41116400-41119200	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr19:41116400-41119200	Weak transcription	Small Intestine	intestine
50	chr19:41116400-41120000	Enhancers	Stomach Mucosa	stomach

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