Variant report

Variant	rs7222646
Chromosome Location	chr17:46185421-46185422
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	TAF1	chr17:46184495-46185473	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr17:46184358-46185635	GM18505	blood:	n/a	n/a
3	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
4	ELF1	chr17:46184544-46185551	A549	lung:	n/a	n/a
5	REST	chr17:46184441-46185884	H1-neurons	neurons:	n/a	chr17:46185226-46185239 chr17:46184991-46185004 chr17:46184987-46185007
6	MAX	chr17:46184468-46185522	ECC-1	luminal epithelium:	n/a	chr17:46185211-46185221 chr17:46184963-46184973 chr17:46185208-46185217
7	JUND	chr17:46184553-46185479	K562	blood:	n/a	chr17:46184858-46184867
8	MAX	chr17:46184452-46185553	K562	blood:	n/a	chr17:46185211-46185221 chr17:46184963-46184973 chr17:46185208-46185217
9	PML	chr17:46184541-46185491	K562	blood:	n/a	n/a
10	FOSL2	chr17:46184391-46185581	A549	lung:	n/a	chr17:46184858-46184867
11	ELF1	chr17:46184867-46185503	A549	lung:	n/a	n/a
12	POLR2A	chr17:46184521-46185488	GM19099	blood:	n/a	n/a
13	POLR2A	chr17:46184390-46185493	U87	brain:	n/a	n/a
14	GABPA	chr17:46184324-46185724	SK-N-SH	brain:	n/a	chr17:46185211-46185220
15	BCL3	chr17:46184370-46185489	A549	lung:	n/a	chr17:46185406-46185415
16	POLR2A	chr17:46184525-46185515	H1-neurons	neurons:	n/a	n/a
17	GABPA	chr17:46184396-46185619	A549	lung:	n/a	chr17:46185211-46185220
18	MAX	chr17:46184675-46185466	Hela-S3	cervix:	n/a	chr17:46185211-46185221 chr17:46184963-46184973 chr17:46185208-46185217
19	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
20	EBF1	chr17:46185024-46185460	GM12878	blood:	n/a	n/a
21	MAZ	chr17:46184601-46185469	K562	blood:	n/a	chr17:46185211-46185221 chr17:46184963-46184973 chr17:46185208-46185217
22	YY1	chr17:46184642-46185524	SK-N-SH_RA	brain:	n/a	chr17:46185208-46185222
23	POLR2A	chr17:46184455-46186110	GM12878	blood:	n/a	n/a
24	POLR2A	chr17:46184399-46185499	HUVEC	blood vessel:	n/a	n/a
25	RUNX3	chr17:46184362-46185772	GM12878	blood:	n/a	n/a
26	POLR2A	chr17:46184427-46185456	K562	blood:	n/a	n/a
27	POLR2A	chr17:46185296-46189875	K562	blood:	n/a	n/a
28	POLR2A	chr17:46184522-46185464	GM18526	blood:	n/a	n/a
29	POLR2A	chr17:46184452-46185546	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr17:46184350-46185517	SK-N-MC	brain:	n/a	n/a
31	YY1	chr17:46184580-46185702	SK-N-SH_RA	brain:	n/a	chr17:46185208-46185222
32	POLR2A	chr17:46184447-46185479	ProgFib	skin:	n/a	n/a
33	BRCA1	chr17:46184621-46185432	HepG2	liver:	n/a	n/a
34	NR2C2	chr17:46184671-46185453	Hela-S3	cervix:	n/a	chr17:46185120-46185129
35	RELA	chr17:46184495-46185883	GM19099	blood:	n/a	n/a
36	BCL3	chr17:46184507-46185436	A549	lung:	n/a	chr17:46185406-46185415
37	ARID3A	chr17:46184659-46185507	HepG2	liver:	n/a	n/a
38	POLR2A	chr17:46184504-46185706	H1-neurons	neurons:	n/a	n/a
39	TAF1	chr17:46184531-46185497	ECC-1	luminal epithelium:	n/a	n/a
40	MAZ	chr17:46184480-46185425	GM12878	blood:	n/a	chr17:46185211-46185221 chr17:46184963-46184973 chr17:46185208-46185217
41	FOXM1	chr17:46184430-46185512	GM12878	blood:	n/a	n/a
42	POLR2A	chr17:46184395-46185484	HCT-116	colon:	n/a	n/a
43	POLR2A	chr17:46184430-46185478	GM12878	blood:	n/a	n/a
44	PML	chr17:46184591-46185425	MCF-7	breast:	n/a	n/a
45	MAX	chr17:46184718-46185458	MCF-7	breast:	n/a	chr17:46185211-46185221 chr17:46184963-46184973 chr17:46185208-46185217
46	POLR2A	chr17:46184401-46185452	GM18951	blood:	n/a	n/a
47	POLR2A	chr17:46184493-46185588	GM12878	blood:	n/a	n/a
48	CREB1	chr17:46184474-46185510	GM12878	blood:	n/a	n/a
49	ELK4	chr17:46184836-46185493	Hela-S3	cervix:	n/a	n/a
50	NFIC	chr17:46184503-46185549	HepG2	liver:	n/a	n/a

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	chr11:62438851..62439470-chr17:46185243..46185807,2	Hela-S3	cervix:
4	chr17:46185336..46187355-chr6:44217982..44220067,2	MCF-7	breast:
5	chr17:46124892..46127654-chr17:46182877..46187326,5	K562	blood:
6	chr17:46123538..46128867-chr17:46183649..46187295,7	MCF-7	breast:
7	chr17:46132648..46135293-chr17:46184683..46187431,2	K562	blood:
8	chr17:46184602..46186632-chr17:46186895..46189927,3	MCF-7	breast:
9	chr17:46124455..46126784-chr17:46185415..46187285,2	MCF-7	breast:
10	chr17:46177349..46182213-chr17:46183318..46186399,5	K562	blood:
11	chr17:46125014..46129511-chr17:46182877..46189561,8	K562	blood:
12	chr17:46174648..46181471-chr17:46183317..46187457,20	MCF-7	breast:
13	chr17:46177349..46180853-chr17:46182060..46186447,10	K562	blood:

Variant related genes	Relation type
SNX11	TF binding region
ENSG00000108468	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000263412	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1010228	0.87[MKK][hapmap]
rs11079806	0.81[ASW][hapmap];0.88[MKK][hapmap]
rs11079808	0.86[MKK][hapmap]
rs11079810	0.88[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11079813	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11650476	0.81[EUR][1000 genomes]
rs11650615	0.88[LWK][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap]
rs11651097	0.87[MKK][hapmap]
rs11654292	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11654342	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11654627	1.00[CHD][hapmap]
rs11658242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12103808	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1468270	0.86[MKK][hapmap]
rs1544597	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1975703	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2051821	0.85[MKK][hapmap]
rs2109984	0.87[MKK][hapmap]
rs2240122	0.87[MKK][hapmap]
rs28481675	0.81[EUR][1000 genomes]
rs4794451	0.87[MKK][hapmap]
rs56258199	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60707285	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60843764	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6504067	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6504114	1.00[CEU][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs6504115	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs6847	0.87[MKK][hapmap]
rs7207553	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7207937	0.80[AMR][1000 genomes]
rs7210671	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7217496	0.87[MKK][hapmap]
rs7219844	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7220398	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7220520	0.87[MKK][hapmap]
rs7221720	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7221897	0.80[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7224155	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7225288	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73322881	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73322886	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73324779	0.81[EUR][1000 genomes]
rs8065670	0.87[MKK][hapmap]
rs8065797	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8067470	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.81[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8071697	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8073220	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8077860	0.85[MKK][hapmap]
rs875065	0.87[MKK][hapmap]
rs9890850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9893110	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9894076	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9899461	0.87[MKK][hapmap]
rs9900074	0.83[YRI][hapmap]
rs9905800	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9907268	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9909922	0.91[AMR][1000 genomes];0.90[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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7222646	HSD17B1	cis	parietal	SCAN
rs7222646	PNPO	Cis_1M	lymphoblastoid	RTeQTL
rs7222646	RUNDC1	cis	cerebellum	SCAN
rs7222646	RP5-890E16.2	cis	Nerve Tibial	GTEx
rs7222646	SNX11	cis	parietal	SCAN

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

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

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