Variant report

Variant	rs8109405
Chromosome Location	chr19:51875946-51875947
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	PAX5	chr19:51875550-51876241	GM12878	blood:	n/a	n/a
2	NFIC	chr19:51875758-51876802	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:51875374-51876557	HL-60	blood:	n/a	n/a
4	ZBTB7A	chr19:51875856-51876120	K562	blood:	n/a	n/a
5	POLR2A	chr19:51875870-51876351	K562	blood:	n/a	n/a
6	RUNX3	chr19:51875527-51876757	GM12878	blood:	n/a	chr19:51876107-51876124
7	MXI1	chr19:51875785-51876375	GM12878	blood:	n/a	n/a
8	MYC	chr19:51875444-51876506	NB4	blood:	n/a	chr19:51875952-51875961
9	YY1	chr19:51875899-51876374	GM12878	blood:	n/a	n/a
10	JUND	chr19:51875926-51876363	K562	blood:	n/a	chr19:51876244-51876253
11	TAF1	chr19:51875827-51876335	GM12878	blood:	n/a	n/a
12	STAT5A	chr19:51875551-51876561	GM12878	blood:	n/a	chr19:51876192-51876201 chr19:51876193-51876202 chr19:51876353-51876360
13	PAX5	chr19:51875837-51876477	GM12878	blood:	n/a	chr19:51876351-51876360
14	POLR2A	chr19:51875838-51876212	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:51875561-51876495	GM12878	blood:	n/a	n/a
16	USF2	chr19:51875839-51876286	GM12878	blood:	n/a	n/a
17	EBF1	chr19:51875853-51876334	GM12878	blood:	n/a	chr19:51876044-51876053
18	ELF1	chr19:51874941-51876693	GM12878	blood:	n/a	n/a
19	FOXM1	chr19:51875765-51876591	GM12878	blood:	n/a	n/a
20	WRNIP1	chr19:51875825-51876380	GM12878	blood:	n/a	n/a
21	EBF1	chr19:51875853-51876509	GM12878	blood:	n/a	chr19:51876044-51876053
22	STAT3	chr19:51875920-51876413	GM12878	blood:	n/a	chr19:51876192-51876201 chr19:51876193-51876202 chr19:51876353-51876360
23	TBL1XR1	chr19:51875612-51876387	GM12878	blood:	n/a	n/a
24	RUNX3	chr19:51875274-51876634	GM12878	blood:	n/a	chr19:51876107-51876124
25	RCOR1	chr19:51875806-51876677	GM12878	blood:	n/a	n/a
26	POU2F2	chr19:51875774-51876449	GM12878	blood:	n/a	chr19:51876034-51876046
27	RELA	chr19:51875936-51876472	GM19193	blood:	n/a	n/a
28	POLR2A	chr19:51875873-51876505	GM15510	blood:	n/a	n/a
29	POLR2A	chr19:51875795-51876231	GM12878	blood:	n/a	n/a
30	BRCA1	chr19:51875934-51876134	GM12878	blood:	n/a	n/a
31	TBP	chr19:51875846-51876425	GM12878	blood:	n/a	n/a
32	ELF1	chr19:51875868-51876377	K562	blood:	n/a	n/a
33	PML	chr19:51875654-51876685	GM12878	blood:	n/a	n/a
34	SPI1	chr19:51875884-51876637	GM12878	blood:	n/a	chr19:51876351-51876358 chr19:51876078-51876091
35	EP300	chr19:51875872-51876438	GM12878	blood:	n/a	chr19:51876308-51876315
36	STAT5A	chr19:51875839-51876384	GM12878	blood:	n/a	chr19:51876192-51876201 chr19:51876193-51876202 chr19:51876353-51876360
37	NFIC	chr19:51875931-51876523	GM12878	blood:	n/a	n/a
38	PBX3	chr19:51875946-51876306	GM12878	blood:	n/a	chr19:51876243-51876252
39	MAZ	chr19:51875789-51876403	GM12878	blood:	n/a	chr19:51875952-51875961
40	SMC3	chr19:51875864-51876215	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:51875623-51876555	GM12891	blood:	n/a	n/a
42	SPI1	chr19:51875804-51876575	GM12891	blood:	n/a	chr19:51876351-51876358 chr19:51876078-51876091
43	PML	chr19:51875874-51876280	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:51875751-51876491	GM12878	blood:	n/a	n/a
45	BCL3	chr19:51875829-51876463	GM12878	blood:	n/a	n/a
46	MTA3	chr19:51875277-51876513	GM12878	blood:	n/a	n/a
47	RELA	chr19:51875936-51876471	GM18951	blood:	n/a	n/a
48	BHLHE40	chr19:51875516-51876463	GM12878	blood:	n/a	n/a
49	POLR2A	chr19:51875926-51875946	GM12878	blood:	n/a	n/a
50	POLR2A	chr19:51875752-51876281	GM12891	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:51875946-51875996	NB4	blood:	n/a
2	chr19:51875946-51875996	HUVEC	blood vessel:	n/a
3	chr19:51875946-51875996	GM19239	blood:	n/a
4	chr19:51875946-51875996	IMR90	lung:	fetal
5	chr19:51875946-51875996	HAEpiC	amniotic membrane:	n/a
6	chr19:51875946-51875996	HPAEpiC	pulmonary alveolar:	n/a
7	chr19:51875946-51875996	HNPCEpiC	eye:	n/a
8	chr19:51875946-51875996	H1-hESC	embryonic stem cell:	embryo
9	chr19:51875946-51875996	NHBE	bronchial:	n/a
10	chr19:51875946-51875996	HRE	kidney:	n/a
11	chr19:51875946-51875996	SK-N-SH_RA	brain:	n/a
12	chr19:51875946-51875996	RPTEC	kidney:	n/a
13	chr19:51875946-51875996	GM12892	blood:	n/a
14	chr19:51875946-51875996	NHDF-neo	bronchial:	n/a
15	chr19:51875946-51875996	HEK293	kidney:	embryo
16	chr19:51875946-51875996	PrEC	prostate:	n/a
17	chr19:51875946-51875996	NT2-D1	testis:	n/a
18	chr19:51875946-51875996	HCM	heart:	n/a
19	chr19:51875946-51875996	HRPEpiC	eye:	n/a
20	chr19:51875946-51875996	AoSMC	blood vessel:	n/a
21	chr19:51875946-51875996	HRCEpiC	kidney:	n/a
22	chr19:51875946-51875996	Hepatocyte	liver:	n/a
23	chr19:51875946-51875996	BE2_C	brain:	n/a
24	chr19:51875946-51875996	BJ	skin:	n/a
25	chr19:51875946-51875996	HCF	heart:	n/a
26	chr19:51875946-51875996	HMEC	breast:	n/a
27	chr19:51875946-51875996	GM12891	blood:	n/a
28	chr19:51875946-51875996	K562	blood:	n/a
29	chr19:51875946-51875996	AG04450	lung:	fetal
30	chr19:51875946-51875996	SAEC	small airway:	n/a
31	chr19:51875946-51875996	Jurkat	blood:	n/a
32	chr19:51875946-51875996	GM06990	blood:	n/a
33	chr19:51875946-51875996	HL-60	blood:	n/a
34	chr19:51875946-51875996	GM12878	blood:	n/a
35	chr19:51875946-51875996	NH-A	brain:	n/a
36	chr19:51875946-51875996	SKMC	muscle:	n/a
37	chr19:51875946-51875996	SK-N-MC	brain:	n/a
38	chr19:51875946-51875996	HIPEpiC	eye:	n/a
39	chr19:51875946-51875996	A549	lung:	n/a
40	chr19:51875946-51875996	AG04449	skin:	fetal
41	chr19:51875946-51875996	ProgFib	skin:	n/a
42	chr19:51875946-51875996	ECC-1	luminal epithelium:	n/a
43	chr19:51875946-51875996	HCPEpiC	choroid plexus:	n/a
44	chr19:51875946-51875996	MCF10A-Er-Src	breast:	n/a
45	chr19:51875946-51875996	AG09309	skin:	n/a
46	chr19:51875946-51875996	CMK	blood:	n/a
47	chr19:51875946-51875996	SK-N-SH	brain:	n/a
48	chr19:51875946-51875996	U87	brain:	n/a
49	chr19:51875946-51875996	PANC-1	pancreas:	n/a
50	chr19:51875946-51875996	Caco-2	colon:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:51868728..51870423-chr19:51874216..51876129,2	MCF-7	breast:

Variant related genes	Relation type
NKG7	TF binding region
ENSG00000269403	TF binding region
CLDND2	TF binding region
ENSG00000269403	CpG island
CLDND2	CpG island
NKG7	CpG island
ENSG00000105379	Chromatin interaction
ENSG00000268520	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10418894	1.00[ASN][1000 genomes]
rs10419337	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420738	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305770	1.00[CHB][hapmap]
rs4082929	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1813225	chr19:51821612-51888813	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv912294	chr19:51844978-51878841	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8109405	NKG7	cis	lymphoblastoid	seeQTL
rs8109405	NKG7	cis	multi-tissue	Pritchard
rs8109405	CLDND2	cis	lymphoblastoid	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51870000-51876800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
2	chr19:51872000-51897000	Weak transcription	Right Atrium	heart
3	chr19:51873600-51876000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
4	chr19:51873600-51876800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr19:51873600-51877000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr19:51873600-51880000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:51873800-51876200	Active TSS	Duodenum Mucosa	Duodenum
8	chr19:51874000-51877000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:51874200-51877000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:51874400-51876600	Enhancers	Primary B cells from cord blood	blood
11	chr19:51874400-51876600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:51874400-51876600	Enhancers	Thymus	Thymus
13	chr19:51874600-51876600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr19:51874600-51876600	Flanking Active TSS	Dnd41	blood
15	chr19:51874600-51877000	Enhancers	Spleen	Spleen
16	chr19:51874800-51876000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr19:51874800-51876000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:51874800-51876400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr19:51875000-51876200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr19:51875000-51876400	Flanking Active TSS	GM12878-XiMat	blood
21	chr19:51875000-51877000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:51875000-51877000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr19:51875200-51876200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:51875200-51876200	Enhancers	Fetal Muscle Trunk	muscle
25	chr19:51875200-51876400	Bivalent Enhancer	HepG2	liver
26	chr19:51875200-51876800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr19:51875400-51876000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:51875400-51876000	Active TSS	Liver	Liver
29	chr19:51875400-51876200	Enhancers	Primary B cells from peripheral blood	blood
30	chr19:51875400-51876200	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr19:51875400-51876400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:51875600-51876000	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr19:51875600-51876800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr19:51875800-51876600	Enhancers	K562	blood
35	chr19:51875800-51876800	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr19:51875800-51877600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:51875800-51878800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr19:51875800-51881200	Enhancers	Fetal Thymus	thymus

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