Variant report

Variant	rs2072441
Chromosome Location	chr17:46185014-46185015
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	TAF1	chr17:46184495-46185473	H1-hESC	embryonic stem cell:	n/a	n/a
2	TAF1	chr17:46184553-46185375	K562	blood:	n/a	n/a
3	CCNT2	chr17:46184695-46185316	K562	blood:	n/a	chr17:46185054-46185063
4	ELF1	chr17:46184792-46185307	K562	blood:	n/a	n/a
5	POLR2A	chr17:46184560-46185397	NB4	blood:	n/a	n/a
6	SP1	chr17:46184419-46185352	GM12878	blood:	n/a	chr17:46185054-46185064 chr17:46185053-46185065 chr17:46185211-46185220 chr17:46185050-46185064 chr17:46185250-46185260 chr17:46185055-46185064 chr17:46185054-46185064 chr17:46185053-46185065 chr17:46185211-46185221 chr17:46185055-46185064 chr17:46185054-46185063 chr17:46185210-46185222 chr17:46185205-46185215 chr17:46184849-46184870 chr17:46185210-46185222 chr17:46185211-46185221 chr17:46185212-46185221
7	PAX5	chr17:46184666-46185265	GM12892	blood:	n/a	n/a
8	ELF1	chr17:46184485-46185395	GM12878	blood:	n/a	n/a
9	YY1	chr17:46184651-46185342	HCT-116	colon:	n/a	chr17:46185208-46185222
10	POLR2A	chr17:46184524-46185396	K562	blood:	n/a	n/a
11	POLR2A	chr17:46184541-46185371	HL-60	blood:	n/a	n/a
12	FOXP2	chr17:46184703-46185295	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr17:46184477-46185414	PANC-1	pancreas:	n/a	n/a
14	TAF1	chr17:46184612-46185367	HepG2	liver:	n/a	n/a
15	POLR2A	chr17:46184358-46185635	GM18505	blood:	n/a	n/a
16	EGR1	chr17:46184664-46185501	ECC-1	luminal epithelium:	n/a	chr17:46185209-46185218 chr17:46185206-46185219 chr17:46185206-46185219 chr17:46185246-46185260 chr17:46185211-46185221 chr17:46185244-46185259 chr17:46185207-46185218 chr17:46185206-46185219 chr17:46185207-46185218 chr17:46185205-46185220 chr17:46185245-46185258 chr17:46185207-46185221 chr17:46185206-46185220 chr17:46185208-46185218 chr17:46185206-46185219 chr17:46185202-46185224 chr17:46185208-46185218 chr17:46185245-46185258
17	GABPA	chr17:46184657-46185325	HepG2	liver:	n/a	chr17:46185211-46185220
18	ELF1	chr17:46184544-46185551	A549	lung:	n/a	n/a
19	SIN3AK20	chr17:46184390-46185324	A549	lung:	n/a	n/a
20	FOXA2	chr17:46184452-46185190	A549	lung:	n/a	n/a
21	REST	chr17:46184441-46185884	H1-neurons	neurons:	n/a	chr17:46185226-46185239 chr17:46184991-46185004 chr17:46184987-46185007
22	MAX	chr17:46184468-46185522	ECC-1	luminal epithelium:	n/a	chr17:46185211-46185221 chr17:46184963-46184973 chr17:46185208-46185217
23	JUND	chr17:46184553-46185479	K562	blood:	n/a	chr17:46184858-46184867
24	SP4	chr17:46184588-46185154	H1-hESC	embryonic stem cell:	n/a	chr17:46185051-46185067 chr17:46184841-46184857
25	MAX	chr17:46184452-46185553	K562	blood:	n/a	chr17:46185211-46185221 chr17:46184963-46184973 chr17:46185208-46185217
26	PML	chr17:46184541-46185491	K562	blood:	n/a	n/a
27	FOSL2	chr17:46184391-46185581	A549	lung:	n/a	chr17:46184858-46184867
28	GABPA	chr17:46184810-46185342	Hela-S3	cervix:	n/a	chr17:46185211-46185220
29	YY1	chr17:46184567-46185346	HepG2	liver:	n/a	chr17:46185208-46185222
30	CTCF	chr17:46184980-46185130	HL-60	blood:	n/a	n/a
31	NRF1	chr17:46184499-46185328	GM12878	blood:	n/a	chr17:46185211-46185220
32	SP1	chr17:46184564-46185159	K562	blood:	n/a	chr17:46185054-46185064 chr17:46185053-46185065 chr17:46185050-46185064 chr17:46185055-46185064 chr17:46185054-46185064 chr17:46185053-46185065 chr17:46185055-46185064 chr17:46185054-46185063 chr17:46184849-46184870
33	ELF1	chr17:46184867-46185503	A549	lung:	n/a	n/a
34	POLR2A	chr17:46184647-46185316	A549	lung:	n/a	n/a
35	ZBTB7A	chr17:46184527-46185293	K562	blood:	n/a	n/a
36	CHD2	chr17:46184680-46185278	HepG2	liver:	n/a	chr17:46185055-46185065
37	POLR2A	chr17:46184521-46185488	GM19099	blood:	n/a	n/a
38	POLR2A	chr17:46184390-46185493	U87	brain:	n/a	n/a
39	PBX3	chr17:46184505-46185389	SK-N-SH	brain:	n/a	chr17:46184859-46184868
40	HMGN3	chr17:46184610-46185328	K562	blood:	n/a	n/a
41	SP1	chr17:46184600-46185067	H1-hESC	embryonic stem cell:	n/a	chr17:46185054-46185064 chr17:46185053-46185065 chr17:46185050-46185064 chr17:46185055-46185064 chr17:46185054-46185064 chr17:46185053-46185065 chr17:46185055-46185064 chr17:46185054-46185063 chr17:46184849-46184870
42	GABPA	chr17:46184324-46185724	SK-N-SH	brain:	n/a	chr17:46185211-46185220
43	BCL3	chr17:46184370-46185489	A549	lung:	n/a	chr17:46185406-46185415
44	POLR2A	chr17:46184525-46185515	H1-neurons	neurons:	n/a	n/a
45	GABPA	chr17:46184396-46185619	A549	lung:	n/a	chr17:46185211-46185220
46	MAX	chr17:46184675-46185466	Hela-S3	cervix:	n/a	chr17:46185211-46185221 chr17:46184963-46184973 chr17:46185208-46185217
47	EGR1	chr17:46184656-46185588	MCF-7	breast:	n/a	chr17:46185209-46185218 chr17:46185206-46185219 chr17:46185206-46185219 chr17:46185246-46185260 chr17:46185211-46185221 chr17:46185244-46185259 chr17:46185207-46185218 chr17:46185206-46185219 chr17:46185207-46185218 chr17:46185205-46185220 chr17:46185245-46185258 chr17:46185207-46185221 chr17:46185206-46185220 chr17:46185208-46185218 chr17:46185206-46185219 chr17:46185202-46185224 chr17:46185208-46185218 chr17:46185245-46185258
48	EP300	chr17:46184764-46185046	GM12878	blood:	n/a	n/a
49	MAZ	chr17:46184601-46185469	K562	blood:	n/a	chr17:46185211-46185221 chr17:46184963-46184973 chr17:46185208-46185217
50	YY1	chr17:46184642-46185524	SK-N-SH_RA	brain:	n/a	chr17:46185208-46185222

No.	Distal block	Cell Line	Cell type
1	chr17:46032611..46035777-chr17:46183682..46186625,3	MCF-7	breast:
2	chr17:46175023..46180196-chr17:46181333..46189268,23	MCF-7	breast:
3	chr17:46048142..46050112-chr17:46183426..46185210,2	K562	blood:
4	chr17:46124892..46127654-chr17:46182877..46187326,5	K562	blood:
5	chr17:46123538..46128867-chr17:46183649..46187295,7	MCF-7	breast:
6	chr17:46132648..46135293-chr17:46184683..46187431,2	K562	blood:
7	chr17:46184602..46186632-chr17:46186895..46189927,3	MCF-7	breast:
8	chr17:46177349..46182213-chr17:46183318..46186399,5	K562	blood:
9	chr17:46125014..46129511-chr17:46182877..46189561,8	K562	blood:
10	chr17:46174648..46181471-chr17:46183317..46187457,20	MCF-7	breast:
11	chr17:46177349..46180853-chr17:46182060..46186447,10	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNX11-4	chr17:46184922-46185200	NONHSAT054382

Variant related genes	Relation type
SNX11	TF binding region
ENSG00000263412	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000108468	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000002919	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12603115	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12603380	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12947089	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs12950225	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12952670	0.81[EUR][1000 genomes]
rs1316657	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs1452666	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs1452667	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs17620033	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs1860862	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs2021752	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs2041572	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs2060876	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs2109982	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs2123341	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs2278868	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs2305433	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs2924257	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs3792692	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs3792694	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs3805370	0.87[CEU][hapmap];0.80[CHB][hapmap]
rs3897986	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs4793779	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs4794447	0.86[CHB][hapmap]
rs62064954	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6504108	0.81[CHB][hapmap]
rs7220768	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs7223867	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs7225550	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs758999	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs8069263	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs8071267	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8072282	0.87[CEU][hapmap];0.81[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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	nsv112217	chr17:46182711-46190093	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2072441	SNX11	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46184000-46185400	Active TSS	Rectal Smooth Muscle	rectum
2	chr17:46184000-46186000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr17:46184200-46185400	Active TSS	Cortex derived primary cultured neurospheres	brain
4	chr17:46184200-46185600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr17:46184200-46185600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr17:46184200-46185600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
7	chr17:46184200-46185600	Active TSS	Brain Germinal Matrix	brain
8	chr17:46184200-46185800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr17:46184200-46185800	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr17:46184200-46185800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr17:46184200-46185800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:46184200-46185800	Active TSS	Muscle Satellite Cultured Cells	--
13	chr17:46184200-46185800	Active TSS	Brain Angular Gyrus	brain
14	chr17:46184200-46185800	Active TSS	Brain Anterior Caudate	brain
15	chr17:46184200-46185800	Active TSS	Brain Substantia Nigra	brain
16	chr17:46184200-46185800	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr17:46184200-46185800	Active TSS	Ovary	ovary
18	chr17:46184200-46186000	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr17:46184200-46186000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr17:46184200-46186000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr17:46184200-46186000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr17:46184200-46186000	Active TSS	Fetal Intestine Large	intestine
23	chr17:46184200-46186000	Active TSS	Psoas Muscle	Psoas
24	chr17:46184200-46186000	Active TSS	HMEC	breast
25	chr17:46184200-46186000	Active TSS	K562	blood
26	chr17:46184200-46186200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:46184200-46186200	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr17:46184200-46186200	Active TSS	Right Atrium	heart
29	chr17:46184200-46186200	Active TSS	HSMMtube	muscle
30	chr17:46184200-46186400	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr17:46184200-46186400	Active TSS	H1 Cell Line	embryonic stem cell
32	chr17:46184200-46186400	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr17:46184200-46186400	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr17:46184200-46186400	Active TSS	NHLF	lung
35	chr17:46184200-46186800	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr17:46184400-46185400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr17:46184400-46185400	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr17:46184400-46185400	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr17:46184400-46185400	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr17:46184400-46185600	Active TSS	Duodenum Mucosa	Duodenum
41	chr17:46184400-46185600	ZNF genes & repeats	Fetal Brain Male	brain
42	chr17:46184400-46185600	Active TSS	Fetal Heart	heart
43	chr17:46184400-46185600	Active TSS	Fetal Kidney	kidney
44	chr17:46184400-46185600	Active TSS	Fetal Lung	lung
45	chr17:46184400-46185600	Active TSS	Small Intestine	intestine
46	chr17:46184400-46185600	Active TSS	Stomach Smooth Muscle	stomach
47	chr17:46184400-46185600	Active TSS	Spleen	Spleen
48	chr17:46184400-46185600	Active TSS	NH-A	brain
49	chr17:46184400-46185800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr17:46184400-46185800	Active TSS	Brain Inferior Temporal Lobe	brain

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