Variant report

Variant	rs9467501
Chromosome Location	chr6:25405157-25405158
allele	G/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	SPI1	chr6:25404999-25405387	GM12891	blood:	n/a	chr6:25405260-25405269
2	ZNF143	chr6:25405020-25405743	GM12878	blood:	n/a	n/a
3	BATF	chr6:25405005-25405442	GM12878	blood:	n/a	n/a
4	YY1	chr6:25404993-25405283	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:25404920-25405392	GM12892	blood:	n/a	n/a
6	SPI1	chr6:25405092-25405453	HL-60	blood:	n/a	chr6:25405260-25405269
7	ELF1	chr6:25404961-25405373	GM12878	blood:	n/a	n/a
8	MEF2A	chr6:25404977-25405636	GM12878	blood:	n/a	chr6:25405455-25405464 chr6:25405459-25405474 chr6:25405450-25405471 chr6:25405454-25405475 chr6:25405459-25405474 chr6:25405450-25405471 chr6:25405454-25405475 chr6:25405457-25405472 chr6:25405452-25405467 chr6:25405454-25405465 chr6:25405461-25405472 chr6:25405460-25405471 chr6:25405458-25405473 chr6:25405452-25405466 chr6:25405457-25405474 chr6:25405450-25405471 chr6:25405459-25405473 chr6:25405454-25405475 chr6:25405461-25405470 chr6:25405458-25405474
9	PAX5	chr6:25404931-25405330	GM12878	blood:	n/a	chr6:25405260-25405269 chr6:25405263-25405272
10	MTA3	chr6:25404914-25405788	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:25404911-25405477	GM12892	blood:	n/a	n/a
12	SMC3	chr6:25404998-25405528	GM12878	blood:	n/a	n/a
13	YY1	chr6:25404878-25405323	GM12878	blood:	n/a	n/a
14	EBF1	chr6:25405051-25405759	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:25404964-25405424	GM12878	blood:	n/a	n/a
16	NFATC1	chr6:25404941-25405472	GM12878	blood:	n/a	n/a
17	RUNX3	chr6:25404912-25405434	GM12878	blood:	n/a	n/a
18	SP1	chr6:25405004-25405444	GM12878	blood:	n/a	n/a
19	BCL11A	chr6:25405030-25405378	GM12878	blood:	n/a	chr6:25405260-25405269
20	TCF12	chr6:25404981-25405417	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:25405089-25405245	GM12878	blood:	n/a	n/a
22	POU2F2	chr6:25404927-25405438	GM12878	blood:	n/a	n/a
23	SPI1	chr6:25404984-25405470	GM12891	blood:	n/a	chr6:25405260-25405269
24	NFIC	chr6:25404897-25406001	GM12878	blood:	n/a	n/a
25	TCF3	chr6:25404979-25405410	GM12878	blood:	n/a	n/a
26	MAZ	chr6:25405056-25405529	GM12878	blood:	n/a	n/a
27	ATF2	chr6:25404958-25405638	GM12878	blood:	n/a	n/a
28	TCF3	chr6:25405029-25405307	GM12878	blood:	n/a	n/a
29	PAX5	chr6:25404937-25405472	GM12878	blood:	n/a	chr6:25405260-25405269 chr6:25405263-25405272
30	MEF2A	chr6:25404990-25405895	GM12878	blood:	n/a	chr6:25405455-25405464 chr6:25405459-25405474 chr6:25405450-25405471 chr6:25405454-25405475 chr6:25405459-25405474 chr6:25405450-25405471 chr6:25405454-25405475 chr6:25405457-25405472 chr6:25405452-25405467 chr6:25405454-25405465 chr6:25405461-25405472 chr6:25405460-25405471 chr6:25405458-25405473 chr6:25405452-25405466 chr6:25405457-25405474 chr6:25405450-25405471 chr6:25405459-25405473 chr6:25405454-25405475 chr6:25405461-25405470 chr6:25405458-25405474
31	SPI1	chr6:25404991-25405438	GM12878	blood:	n/a	chr6:25405260-25405269
32	PAX5	chr6:25405047-25405330	GM12878	blood:	n/a	chr6:25405260-25405269 chr6:25405263-25405272
33	NFATC1	chr6:25405080-25405488	GM12878	blood:	n/a	n/a
34	CHD2	chr6:25405045-25405509	GM12878	blood:	n/a	n/a
35	IRF4	chr6:25404923-25405530	GM12878	blood:	n/a	n/a
36	POLR2A	chr6:25405085-25405218	GM12878	blood:	n/a	n/a
37	BCLAF1	chr6:25404994-25405468	GM12878	blood:	n/a	chr6:25405260-25405269
38	SPI1	chr6:25405115-25405388	GM12878	blood:	n/a	chr6:25405260-25405269
39	MTA3	chr6:25405029-25405830	GM12878	blood:	n/a	n/a
40	WRNIP1	chr6:25405043-25405363	GM12878	blood:	n/a	n/a
41	BCL3	chr6:25405108-25405464	GM12878	blood:	n/a	chr6:25405260-25405269
42	PML	chr6:25404914-25405879	GM12878	blood:	n/a	n/a
43	BCL11A	chr6:25405019-25405472	GM12878	blood:	n/a	chr6:25405260-25405269
44	BCLAF1	chr6:25405013-25405950	GM12878	blood:	n/a	chr6:25405260-25405269 chr6:25405801-25405810
45	FOXM1	chr6:25404944-25405595	GM12878	blood:	n/a	n/a
46	IRF4	chr6:25404914-25405466	GM12878	blood:	n/a	n/a
47	STAT1	chr6:25405073-25405396	GM12878	blood:	n/a	chr6:25405085-25405096
48	RUNX3	chr6:25404863-25406226	GM12878	blood:	n/a	n/a
49	MEF2C	chr6:25405016-25405688	GM12878	blood:	n/a	chr6:25405455-25405464 chr6:25405459-25405474 chr6:25405450-25405471 chr6:25405454-25405475 chr6:25405459-25405474 chr6:25405450-25405471 chr6:25405454-25405475 chr6:25405457-25405472 chr6:25405452-25405467 chr6:25405454-25405465 chr6:25405461-25405472 chr6:25405460-25405471 chr6:25405458-25405473 chr6:25405452-25405466 chr6:25405457-25405474 chr6:25405450-25405471 chr6:25405459-25405473 chr6:25405454-25405475 chr6:25405461-25405470 chr6:25405458-25405474
50	PBX3	chr6:25405056-25405260	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000253017	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10946770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201737	1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs716796	0.81[EUR][1000 genomes]
rs716798	0.81[EUR][1000 genomes]
rs880225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461152	0.81[EUR][1000 genomes]
rs9461153	0.83[EUR][1000 genomes]

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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9467501	LRRC16	Cis_1M	lymphoblastoid	RTeQTL
rs9467501	LRRC16	cis	multi-tissue	Pritchard

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25377400-25410600	Weak transcription	Gastric	stomach
2	chr6:25397600-25405600	Weak transcription	Stomach Mucosa	stomach
3	chr6:25399000-25405200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:25402200-25405200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr6:25402200-25405200	Weak transcription	HMEC	breast
6	chr6:25402200-25406200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:25402200-25409600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:25403600-25405200	Enhancers	Lung	lung
9	chr6:25403600-25405200	Enhancers	Right Atrium	heart
10	chr6:25403600-25405200	Enhancers	Small Intestine	intestine
11	chr6:25403600-25406000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:25403600-25406400	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr6:25403600-25408200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr6:25403800-25405200	Enhancers	H1 Cell Line	embryonic stem cell
15	chr6:25403800-25406000	Enhancers	Brain Substantia Nigra	brain
16	chr6:25403800-25406400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:25403800-25406400	Weak transcription	Spleen	Spleen
18	chr6:25403800-25410600	Weak transcription	Pancreas	Pancrea
19	chr6:25404200-25405200	Active TSS	Rectal Smooth Muscle	rectum
20	chr6:25404200-25406000	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr6:25404400-25405200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:25404400-25405200	Enhancers	Fetal Muscle Leg	muscle
23	chr6:25404400-25406400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr6:25404400-25406600	Enhancers	Colonic Mucosa	Colon
25	chr6:25404400-25406600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr6:25404400-25407400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:25404400-25407600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:25404400-25410800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:25404600-25406000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:25404800-25405200	Active TSS	Primary T cells from cord blood	blood
31	chr6:25404800-25405200	Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr6:25404800-25405400	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr6:25404800-25405600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr6:25404800-25405600	Active TSS	Thymus	Thymus
35	chr6:25404800-25405800	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr6:25404800-25405800	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr6:25404800-25405800	Flanking Active TSS	Fetal Thymus	thymus
38	chr6:25404800-25406000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:25404800-25406600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:25405000-25405200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr6:25405000-25405200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr6:25405000-25405200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr6:25405000-25405200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:25405000-25405200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr6:25405000-25405200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:25405000-25405200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:25405000-25405200	Active TSS	Brain Hippocampus Middle	brain
48	chr6:25405000-25405200	Enhancers	Fetal Lung	lung
49	chr6:25405000-25405200	Flanking Bivalent TSS/Enh	Dnd41	blood
50	chr6:25405000-25405200	Flanking Active TSS	GM12878-XiMat	blood

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