Variant report

Variant	rs2270180
Chromosome Location	chr17:17185102-17185103
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	GABPA	chr17:17183697-17185174	A549	lung:	n/a	n/a
2	CHD2	chr17:17183906-17185110	K562	blood:	n/a	chr17:17184198-17184208
3	GATA3	chr17:17183800-17185157	A549	lung:	n/a	n/a
4	KAP1	chr17:17184337-17185257	U2OS	brain:	n/a	n/a
5	POLR2A	chr17:17183720-17185169	H1-hESC	embryonic stem cell:	n/a	n/a
6	ELF1	chr17:17184345-17185113	A549	lung:	n/a	chr17:17184692-17184705
7	TCF12	chr17:17183700-17185248	A549	lung:	n/a	n/a
8	POLR2A	chr17:17183723-17185127	U87	brain:	n/a	n/a
9	GABPA	chr17:17183811-17185106	SK-N-SH	brain:	n/a	n/a
10	MAX	chr17:17183773-17185115	ECC-1	luminal epithelium:	n/a	chr17:17184192-17184202 chr17:17184665-17184674 chr17:17184669-17184678
11	ZNF263	chr17:17183893-17185110	HEK293-T-REx	kidney:	n/a	n/a
12	CREB1	chr17:17183813-17185174	GM12878	blood:	n/a	n/a
13	REST	chr17:17183790-17185132	A549	lung:	n/a	chr17:17184022-17184032
14	CTCF	chr17:17184980-17185130	GM12873	blood:	n/a	n/a
15	MAZ	chr17:17183827-17185170	IMR90	lung:	n/a	chr17:17184192-17184202 chr17:17184665-17184674 chr17:17184669-17184678
16	RELA	chr17:17183875-17185149	GM10847	blood:	n/a	n/a
17	POLR2A	chr17:17184307-17185161	HCT-116	colon:	n/a	n/a
18	POLR2A	chr17:17183781-17185374	MCF10A-Er-Src	breast:	n/a	n/a
19	RUNX3	chr17:17184290-17185231	GM12878	blood:	n/a	n/a
20	SIX5	chr17:17184082-17185388	A549	lung:	n/a	n/a
21	MAX	chr17:17183729-17185251	A549	lung:	n/a	chr17:17184192-17184202 chr17:17184665-17184674 chr17:17184669-17184678
22	POLR2A	chr17:17183785-17185147	K562	blood:	n/a	n/a
23	MAX	chr17:17183981-17185108	K562	blood:	n/a	chr17:17184192-17184202 chr17:17184665-17184674 chr17:17184669-17184678
24	REST	chr17:17184506-17185240	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr17:17183705-17185113	GM12878	blood:	n/a	n/a
26	MTA3	chr17:17183698-17185264	GM12878	blood:	n/a	n/a
27	REST	chr17:17183485-17185580	H1-neurons	neurons:	n/a	chr17:17184022-17184032
28	ZBTB33	chr17:17183774-17185212	A549	lung:	n/a	chr17:17184591-17184601 chr17:17184588-17184603
29	POLR2A	chr17:17183698-17185131	GM12878	blood:	n/a	n/a
30	SP1	chr17:17183758-17185125	A549	lung:	n/a	chr17:17184195-17184209 chr17:17184561-17184573 chr17:17184198-17184210 chr17:17184198-17184210 chr17:17184199-17184208
31	POLR2A	chr17:17183807-17185152	Raji	blood:	n/a	n/a
32	POLR2A	chr17:17183841-17185106	HL-60	blood:	n/a	n/a
33	TAF1	chr17:17183778-17185113	A549	lung:	n/a	n/a
34	MXI1	chr17:17183628-17185757	SK-N-SH	brain:	n/a	chr17:17184665-17184680 chr17:17184663-17184678
35	POLR2A	chr17:17183691-17185175	H1-neurons	neurons:	n/a	n/a
36	PML	chr17:17183644-17185151	GM12878	blood:	n/a	n/a
37	MYC	chr17:17183899-17185176	NB4	blood:	n/a	chr17:17184192-17184202 chr17:17184665-17184674 chr17:17184669-17184678
38	POLR2A	chr17:17183792-17185155	PBDE	blood:	n/a	n/a
39	TBP	chr17:17183860-17185145	GM12878	blood:	n/a	n/a
40	POLR2A	chr17:17183789-17185143	GM12892	blood:	n/a	n/a
41	PBX3	chr17:17183835-17185209	A549	lung:	n/a	n/a
42	RUNX3	chr17:17184301-17185178	GM12878	blood:	n/a	n/a
43	CUX1	chr17:17184367-17185245	K562	blood:	n/a	chr17:17185132-17185141
44	HCFC1	chr17:17183706-17185296	Hela-S3	cervix:	n/a	n/a
45	MXI1	chr17:17183718-17185149	IMR90	lung:	n/a	chr17:17184665-17184680 chr17:17184663-17184678
46	ARID3A	chr17:17184122-17185110	HepG2	liver:	n/a	n/a
47	TAF1	chr17:17183809-17185124	ECC-1	luminal epithelium:	n/a	n/a
48	CREB1	chr17:17183821-17185149	HepG2	liver:	n/a	n/a
49	SIN3AK20	chr17:17183723-17185186	MCF-7	breast:	n/a	n/a
50	POLR2A	chr17:17183816-17185120	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:17185060-17185110	GM19239	blood:	n/a
2	chr17:17185060-17185110	ovcar-3	ovarian:	n/a
3	chr17:17185060-17185110	HRPEpiC	eye:	n/a
4	chr17:17185060-17185110	Hepatocyte	liver:	n/a
5	chr17:17185060-17185110	CMK	blood:	n/a
6	chr17:17185060-17185110	NB4	blood:	n/a
7	chr17:17185060-17185110	HCPEpiC	choroid plexus:	n/a
8	chr17:17185060-17185110	HPAEpiC	pulmonary alveolar:	n/a
9	chr17:17185060-17185110	HRE	kidney:	n/a
10	chr17:17185060-17185110	IMR90	lung:	fetal
11	chr17:17185060-17185110	PANC-1	pancreas:	n/a
12	chr17:17185060-17185110	HCM	heart:	n/a
13	chr17:17185060-17185110	Jurkat	blood:	n/a
14	chr17:17185060-17185110	ECC-1	luminal epithelium:	n/a
15	chr17:17185060-17185110	GM06990	blood:	n/a
16	chr17:17185060-17185110	NH-A	brain:	n/a
17	chr17:17185060-17185110	HAEpiC	amniotic membrane:	n/a
18	chr17:17185060-17185110	HepG2	liver:	n/a
19	chr17:17185060-17185110	SAEC	small airway:	n/a
20	chr17:17185060-17185110	U87	brain:	n/a
21	chr17:17185060-17185110	NHDF-neo	bronchial:	n/a
22	chr17:17185060-17185110	AG04450	lung:	fetal
23	chr17:17185060-17185110	MCF-7	breast:	n/a
24	chr17:17185060-17185110	PFSK-1	brain:	n/a
25	chr17:17185060-17185110	HNPCEpiC	eye:	n/a
26	chr17:17185060-17185110	Caco-2	colon:	n/a
27	chr17:17185060-17185110	AG04449	skin:	fetal
28	chr17:17185060-17185110	K562	blood:	n/a
29	chr17:17185060-17185110	GM12892	blood:	n/a
30	chr17:17185060-17185110	HMEC	breast:	n/a
31	chr17:17185060-17185110	SKMC	muscle:	n/a
32	chr17:17185060-17185110	HL-60	blood:	n/a
33	chr17:17185060-17185110	HEEpiC	esophagus:	n/a
34	chr17:17185060-17185110	AoSMC	blood vessel:	n/a
35	chr17:17185060-17185110	HRCEpiC	kidney:	n/a
36	chr17:17185060-17185110	T-47D	breast:	n/a
37	chr17:17185060-17185110	HIPEpiC	eye:	n/a
38	chr17:17185060-17185110	RPTEC	kidney:	n/a
39	chr17:17185060-17185110	NHBE	bronchial:	n/a
40	chr17:17185060-17185110	NT2-D1	testis:	n/a
41	chr17:17185060-17185110	AG10803	skin:	n/a
42	chr17:17185060-17185110	HUVEC	blood vessel:	n/a
43	chr17:17185060-17185110	SK-N-SH_RA	brain:	n/a
44	chr17:17185060-17185110	BJ	skin:	n/a
45	chr17:17185060-17185110	SK-N-MC	brain:	n/a
46	chr17:17185060-17185110	A549	lung:	n/a
47	chr17:17185060-17185110	HEK293	kidney:	embryo
48	chr17:17185060-17185110	HCF	heart:	n/a
49	chr17:17185060-17185110	Hela-S3	cervix:	n/a
50	chr17:17185060-17185110	GM12878	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:17182421..17186483-chr17:17204152..17209830,5	MCF-7	breast:
2	chr17:17138280..17141930-chr17:17183181..17187644,4	MCF-7	breast:
3	chr17:17139508..17142367-chr17:17182538..17186121,3	MCF-7	breast:
4	chr17:17183415..17186229-chr17:17206165..17209020,3	MCF-7	breast:
5	chr17:17183059..17186537-chr17:17204352..17209458,5	K562	blood:
6	chr17:17132573..17135085-chr17:17184051..17185920,2	K562	blood:
7	chr17:17181690..17186423-chr17:17204352..17210529,13	K562	blood:
8	chr17:17173847..17176636-chr17:17182577..17185189,4	MCF-7	breast:

Variant related genes	Relation type
COPS3	TF binding region
COPS3	CpG island
ENSG00000154803	Chromatin interaction
ENSG00000266498	Chromatin interaction
ENSG00000264187	Chromatin interaction
ENSG00000141030	Chromatin interaction
ENSG00000205309	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1124961	1.00[ASW][hapmap]
rs12600635	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs12601848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602831	0.91[ASN][1000 genomes]
rs12602871	0.91[ASN][1000 genomes]
rs16961474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16961493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16961507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2294155	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34518797	0.91[ASN][1000 genomes]
rs35534166	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3744124	0.80[JPT][hapmap]
rs41283373	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41337846	0.91[ASN][1000 genomes]
rs55689224	0.91[ASN][1000 genomes]
rs6502565	0.87[ASN][1000 genomes]
rs7213351	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219012	0.90[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7222600	0.80[JPT][hapmap]
rs7222697	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7225789	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7226227	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8065774	0.91[ASN][1000 genomes]
rs8070995	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8075526	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8079562	0.91[ASN][1000 genomes]
rs9890243	0.93[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs9896078	0.93[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833380	chr17:17088416-17241206	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1065811	chr17:17104760-17225204	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv833382	chr17:17124329-17305683	Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv469777	chr17:17127385-17272698	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv482546	chr17:17127385-17272698	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv9499	chr17:17181611-17187670	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2270180	PMP22	cis	cerebellum	SCAN
rs2270180	FLCN	cis	Artery Tibial	GTEx
rs2270180	FLCN	cis	cerebellum	SCAN
rs2270180	FLCN	cis	lymphoblastoid	seeQTL
rs2270180	NT5M	cis	Whole Blood	GTEx
rs2270180	PLD6	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17183000-17185200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:17183200-17185200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr17:17183200-17185200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:17183200-17185200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:17183200-17185200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr17:17183200-17185400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:17183200-17185400	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr17:17183200-17185400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr17:17183400-17185200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr17:17183400-17185200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr17:17183400-17185200	Active TSS	Ovary	ovary
12	chr17:17183400-17185200	Active TSS	Pancreas	Pancrea
13	chr17:17183400-17185200	Active TSS	Psoas Muscle	Psoas
14	chr17:17183400-17185200	Active TSS	Right Ventricle	heart
15	chr17:17183400-17185400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr17:17183400-17185400	Active TSS	Brain Anterior Caudate	brain
17	chr17:17183400-17185400	Active TSS	Fetal Kidney	kidney
18	chr17:17183600-17185200	Active TSS	H1 Cell Line	embryonic stem cell
19	chr17:17183600-17185200	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr17:17183600-17185200	Active TSS	Fetal Intestine Small	intestine
21	chr17:17183600-17185400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr17:17183600-17185400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr17:17183800-17185200	Active TSS	Fetal Muscle Trunk	muscle
24	chr17:17183800-17185400	Active TSS	Fetal Brain Male	brain
25	chr17:17184600-17185200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr17:17184600-17185200	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr17:17184600-17185200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr17:17184600-17185200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr17:17184600-17185200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr17:17184600-17185200	Active TSS	Right Atrium	heart
31	chr17:17184600-17185200	Flanking Active TSS	HSMM	muscle
32	chr17:17184600-17185400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr17:17184800-17185200	Flanking Active TSS	H9 Cell Line	embryonic stem cell
34	chr17:17184800-17185200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr17:17184800-17185200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr17:17184800-17185200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr17:17184800-17185200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr17:17184800-17185200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr17:17184800-17185200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
40	chr17:17184800-17185200	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr17:17184800-17185200	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr17:17184800-17185200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr17:17184800-17185200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr17:17184800-17185200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr17:17184800-17185200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr17:17184800-17185200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr17:17184800-17185200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr17:17184800-17185200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr17:17184800-17185200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr17:17184800-17185200	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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