Variant report

Variant	rs12602010
Chromosome Location	chr17:46126116-46126117
allele	A/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	ELF1	chr17:46124903-46126424	MCF-7	breast:	n/a	chr17:46125628-46125640 chr17:46125756-46125765 chr17:46125751-46125763 chr17:46125225-46125237
2	SIN3A	chr17:46124524-46126657	H1-hESC	embryonic stem cell:	n/a	chr17:46125164-46125177 chr17:46125047-46125061
3	POLR2A	chr17:46124277-46126855	GM12892	blood:	n/a	n/a
4	MYC	chr17:46124582-46126769	A549	lung:	n/a	chr17:46125917-46125927 chr17:46125705-46125715 chr17:46125209-46125219 chr17:46125627-46125637
5	PAX5	chr17:46125538-46126274	GM12892	blood:	n/a	n/a
6	MXI1	chr17:46124653-46126572	Hela-S3	cervix:	n/a	n/a
7	MAX	chr17:46124297-46126790	A549	lung:	n/a	chr17:46125917-46125927 chr17:46125705-46125715 chr17:46125209-46125219 chr17:46125627-46125637
8	POLR2A	chr17:46124898-46126618	HCT-116	colon:	n/a	n/a
9	E2F6	chr17:46124520-46126346	A549	lung:	n/a	chr17:46125707-46125716 chr17:46125707-46125719 chr17:46125916-46125925
10	POU2F2	chr17:46126076-46126831	GM12891	blood:	n/a	chr17:46126671-46126682 chr17:46126673-46126682 chr17:46126654-46126664 chr17:46126673-46126683 chr17:46126671-46126682 chr17:46126673-46126683 chr17:46126674-46126681 chr17:46126647-46126669 chr17:46126668-46126686 chr17:46126672-46126682 chr17:46126673-46126681 chr17:46126670-46126685
11	TCF12	chr17:46125998-46126597	A549	lung:	n/a	n/a
12	POLR2A	chr17:46124467-46126786	K562	blood:	n/a	n/a
13	FOXA1	chr17:46125265-46126699	HepG2	liver:	n/a	chr17:46126388-46126403
14	SP1	chr17:46124920-46126177	H1-hESC	embryonic stem cell:	n/a	chr17:46126094-46126106 chr17:46125469-46125490 chr17:46125499-46125511 chr17:46125912-46125926 chr17:46126095-46126104 chr17:46125915-46125927 chr17:46125965-46125977 chr17:46126094-46126106 chr17:46125501-46125510 chr17:46125703-46125717 chr17:46125708-46125717 chr17:46126096-46126105 chr17:46125707-46125716 chr17:46126075-46126084 chr17:46125915-46125927 chr17:46125708-46125717 chr17:46125706-46125718 chr17:46126095-46126105 chr17:46125916-46125925 chr17:46125706-46125718
15	MAX	chr17:46124675-46126630	GM12878	blood:	n/a	chr17:46125917-46125927 chr17:46125705-46125715 chr17:46125209-46125219 chr17:46125627-46125637
16	TEAD4	chr17:46126025-46126650	HepG2	liver:	n/a	n/a
17	REST	chr17:46125619-46126328	SK-N-SH	brain:	n/a	n/a
18	EP300	chr17:46125214-46126612	HepG2	liver:	n/a	chr17:46125913-46125929 chr17:46125920-46125929 chr17:46126393-46126403 chr17:46125747-46125763 chr17:46126369-46126378 chr17:46125864-46125880
19	BCLAF1	chr17:46126078-46126814	GM12878	blood:	n/a	n/a
20	CEBPD	chr17:46125838-46126310	HepG2	liver:	n/a	n/a
21	EP300	chr17:46124874-46126598	ECC-1	luminal epithelium:	n/a	chr17:46125913-46125929 chr17:46125920-46125929 chr17:46126393-46126403 chr17:46125747-46125763 chr17:46126369-46126378 chr17:46125864-46125880
22	ELF1	chr17:46124686-46126195	A549	lung:	n/a	chr17:46125628-46125640 chr17:46125756-46125765 chr17:46125751-46125763 chr17:46125225-46125237
23	TAF1	chr17:46124745-46126490	ECC-1	luminal epithelium:	n/a	n/a
24	TAF1	chr17:46124607-46126505	H1-hESC	embryonic stem cell:	n/a	n/a
25	TAF1	chr17:46124597-46126549	H1-hESC	embryonic stem cell:	n/a	n/a
26	ZBTB7A	chr17:46125618-46126285	K562	blood:	n/a	n/a
27	FOSL2	chr17:46126080-46126615	A549	lung:	n/a	n/a
28	POU2F2	chr17:46126078-46126338	GM12878	blood:	n/a	n/a
29	FOXA2	chr17:46125002-46126764	A549	lung:	n/a	n/a
30	TAF1	chr17:46125983-46126725	GM12878	blood:	n/a	n/a
31	NFIC	chr17:46125977-46126800	GM12878	blood:	n/a	n/a
32	EP300	chr17:46125302-46126141	SK-N-SH_RA	brain:	n/a	chr17:46125913-46125929 chr17:46125920-46125929 chr17:46125747-46125763 chr17:46125864-46125880
33	MXI1	chr17:46124943-46126595	HepG2	liver:	n/a	n/a
34	E2F6	chr17:46124767-46126152	A549	lung:	n/a	chr17:46125707-46125716 chr17:46125707-46125719 chr17:46125916-46125925
35	TBP	chr17:46125177-46126657	HepG2	liver:	n/a	n/a
36	POLR2A	chr17:46124552-46126631	K562	blood:	n/a	n/a
37	HDAC2	chr17:46125675-46126589	HepG2	liver:	n/a	chr17:46126393-46126402
38	RELA	chr17:46124707-46126736	GM15510	blood:	n/a	n/a
39	POLR2A	chr17:46124715-46126831	GM12892	blood:	n/a	n/a
40	PML	chr17:46126037-46126712	GM12878	blood:	n/a	n/a
41	MAFK	chr17:46125070-46126730	Hela-S3	cervix:	n/a	chr17:46125227-46125242 chr17:46125139-46125154
42	CBX3	chr17:46124720-46126164	K562	blood:	n/a	n/a
43	POLR2A	chr17:46124024-46126770	PFSK-1	brain:	n/a	n/a
44	YY1	chr17:46124759-46126694	GM12891	blood:	n/a	chr17:46125747-46125761 chr17:46125178-46125186 chr17:46125179-46125189 chr17:46125674-46125685 chr17:46125180-46125188 chr17:46125167-46125189 chr17:46125756-46125765 chr17:46125172-46125191 chr17:46125913-46125927 chr17:46125626-46125640 chr17:46125744-46125758 chr17:46125974-46125988 chr17:46125975-46125989 chr17:46125707-46125716 chr17:46125171-46125191
45	GABPA	chr17:46124399-46126523	MCF-7	breast:	n/a	chr17:46125707-46125716
46	TFAP2C	chr17:46125018-46126617	Hela-S3	cervix:	n/a	chr17:46126244-46126259
47	FOXM1	chr17:46126029-46126779	GM12878	blood:	n/a	n/a
48	MAZ	chr17:46125266-46126579	HepG2	liver:	n/a	chr17:46125917-46125927 chr17:46125705-46125715 chr17:46125627-46125637
49	POU2F2	chr17:46126022-46126777	GM12878	blood:	n/a	chr17:46126671-46126682 chr17:46126673-46126682 chr17:46126654-46126664 chr17:46126673-46126683 chr17:46126671-46126682 chr17:46126673-46126683 chr17:46126674-46126681 chr17:46126647-46126669 chr17:46126668-46126686 chr17:46126672-46126682 chr17:46126673-46126681 chr17:46126670-46126685
50	YY1	chr17:46124390-46126614	A549	lung:	n/a	chr17:46125747-46125761 chr17:46125178-46125186 chr17:46125179-46125189 chr17:46125674-46125685 chr17:46125180-46125188 chr17:46125167-46125189 chr17:46125756-46125765 chr17:46125172-46125191 chr17:46125913-46125927 chr17:46125626-46125640 chr17:46125744-46125758 chr17:46125974-46125988 chr17:46125975-46125989 chr17:46125707-46125716 chr17:46125171-46125191

No.	Distal block	Cell Line	Cell type
1	chr17:46124778..46127532-chr17:46702734..46705232,2	K562	blood:
2	chr17:46048551..46050173-chr17:46123931..46126830,2	MCF-7	breast:
3	chr17:46125014..46129511-chr17:46182877..46189561,8	K562	blood:
4	chr17:46126014..46126580-chr6:33359371..33360164,2	Hela-S3	cervix:
5	chr16:778050..778601-chr17:46125207..46126150,2	HCT-116	colon:
6	chr17:46123351..46126971-chr17:46177351..46182209,7	K562	blood:
7	chr17:45972440..45974489-chr17:46124453..46126583,3	MCF-7	breast:
8	chr1:150551298..150552051-chr17:46125500..46126482,2	Hela-S3	cervix:
9	chr17:46126073..46126579-chr20:57466072..57467014,2	NB4	blood:
10	chr17:46034205..46036701-chr17:46124057..46126410,2	MCF-7	breast:
11	chr17:46125721..46126711-chr6:53659755..53660427,2	Hela-S3	cervix:
12	chr17:45769138..45771658-chr17:46124750..46126805,2	MCF-7	breast:
13	chr13:111367301..111368124-chr17:46124980..46126198,4	Hela-S3	cervix:
14	chr17:46125859..46126413-chr8:145149870..145150452,2	HCT-116	colon:
15	chr17:46125881..46126383-chr9:139743677..139744378,2	Hela-S3	cervix:
16	chr17:46125643..46126508-chr9:6015325..6015860,2	HCT-116	colon:
17	chr1:25756460..25757141-chr17:46126080..46126905,2	Hela-S3	cervix:
18	chr17:46124892..46127654-chr17:46182877..46187326,5	K562	blood:
19	chr17:46124025..46127922-chr17:46176725..46180326,7	MCF-7	breast:
20	chr17:46123925..46127532-chr17:46701622..46704234,4	K562	blood:
21	chr17:46125747..46126559-chr7:102984757..102985280,2	Hela-S3	cervix:
22	chr17:46043414..46046355-chr17:46124548..46126704,2	MCF-7	breast:
23	chr17:46048370..46050701-chr17:46124898..46126529,2	K562	blood:
24	chr17:46126011..46126583-chr9:139622137..139622713,2	HCT-116	colon:
25	chr17:46125402..46127552-chr17:46984446..46987320,2	K562	blood:
26	chr1:109642731..109643249-chr17:46125756..46126607,2	HCT-116	colon:
27	chr17:46125418..46126971-chr17:46177352..46179960,2	K562	blood:
28	chr17:46125348..46126346-chr2:29117456..29118040,2	Hela-S3	cervix:
29	chr17:46125724..46126322-chr5:176853595..176854321,2	Hela-S3	cervix:
30	chr17:46126076..46126786-chr7:112090237..112090948,2	Hela-S3	cervix:
31	chr17:46125740..46126287-chr7:129251351..129251902,2	HCT-116	colon:
32	chr17:46124943..46127247-chr17:46188061..46189641,2	K562	blood:
33	chr17:46047400..46050259-chr17:46124707..46126731,3	MCF-7	breast:
34	chr17:46125701..46126210-chr5:90676283..90676951,2	Hela-S3	cervix:
35	chr17:46114300..46116159-chr17:46124838..46126678,3	K562	blood:
36	chr17:46123538..46128867-chr17:46183649..46187295,7	MCF-7	breast:
37	chr17:46125631..46126596-chr17:79196680..79197263,2	HCT-116	colon:
38	chr17:46021116..46023804-chr17:46125669..46127456,2	K562	blood:
39	chr17:46125615..46126602-chr6:26157717..26158637,2	Hela-S3	cervix:
40	chr17:46125363..46126169-chr20:30192598..30193409,2	Hela-S3	cervix:
41	chr17:46122869..46127022-chr17:46176971..46180616,11	MCF-7	breast:
42	chr17:46124694..46126922-chr17:46984422..46985932,2	MCF-7	breast:

Variant related genes	Relation type
NFE2L1	TF binding region
ENSG00000263412	TF binding region
ENSG00000170689	Chromatin interaction
ENSG00000163811	Chromatin interaction
ENSG00000263798	Chromatin interaction
ENSG00000103253	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000273329	Chromatin interaction
ENSG00000207947	Chromatin interaction
ENSG00000087460	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000198055	Chromatin interaction
ENSG00000054148	Chromatin interaction
ENSG00000005243	Chromatin interaction
ENSG00000198933	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000141577	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000106459	Chromatin interaction
ENSG00000137269	Chromatin interaction
ENSG00000248278	Chromatin interaction
ENSG00000137040	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000105821	Chromatin interaction
ENSG00000179091	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000159202	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000108468	Chromatin interaction
ENSG00000006652	Chromatin interaction
ENSG00000233016	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000270066	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000188672	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11079811	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11079812	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11868509	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12449324	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12947056	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12948653	0.89[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs1316643	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs17619103	0.89[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2107308	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2525103	0.84[CEU][hapmap]
rs33983467	0.86[ASN][1000 genomes]
rs62064917	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs62064918	0.86[AMR][1000 genomes]
rs7209484	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7215582	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs8065464	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8081209	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs8438	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12602010	RPRML	cis	parietal	SCAN
rs12602010	NAGLU	cis	parietal	SCAN
rs12602010	KLHL11	cis	cerebellum	SCAN
rs12602010	KRT13	cis	parietal	SCAN
rs12602010	KRT33A	cis	parietal	SCAN
rs12602010	PNPO	cis	parietal	SCAN
rs12602010	PNPO	cis	cerebellum	SCAN
rs12602010	ASB16	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46123600-46127200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr17:46123800-46127000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:46123800-46127600	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr17:46124000-46127200	Active TSS	H1 Cell Line	embryonic stem cell
5	chr17:46124000-46127200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr17:46124000-46127200	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr17:46124200-46126800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:46124200-46127200	Active TSS	GM12878-XiMat	blood
9	chr17:46124200-46127400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr17:46124200-46128000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr17:46124200-46128400	Active TSS	HSMMtube	muscle
12	chr17:46124400-46126400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:46124400-46126800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr17:46124400-46127200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr17:46124400-46127200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr17:46124400-46127400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr17:46124400-46127400	Active TSS	H9 Cell Line	embryonic stem cell
18	chr17:46124400-46127600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr17:46124400-46127600	Active TSS	Right Ventricle	heart
20	chr17:46124400-46127800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr17:46124400-46128200	Active TSS	Left Ventricle	heart
22	chr17:46124400-46132200	Active TSS	Psoas Muscle	Psoas
23	chr17:46124600-46126200	Active TSS	Fetal Brain Male	brain
24	chr17:46124600-46126200	Active TSS	Fetal Brain Female	brain
25	chr17:46124600-46126200	Active TSS	Thymus	Thymus
26	chr17:46124600-46126400	Active TSS	Brain Germinal Matrix	brain
27	chr17:46124600-46126400	Active TSS	Gastric	stomach
28	chr17:46124600-46126600	Active TSS	Fetal Stomach	stomach
29	chr17:46124600-46126800	Active TSS	Esophagus	oesophagus
30	chr17:46124600-46127000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr17:46124600-46127000	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr17:46124600-46127000	Active TSS	Brain Cingulate Gyrus	brain
33	chr17:46124600-46127200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr17:46124600-46127200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr17:46124600-46127200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr17:46124600-46127200	Active TSS	Aorta	Aorta
37	chr17:46124600-46127200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr17:46124600-46127200	Active TSS	K562	blood
39	chr17:46124600-46127400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr17:46124600-46127400	Active TSS	Ovary	ovary
41	chr17:46124600-46127600	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr17:46124600-46127600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr17:46124600-46127800	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr17:46124600-46128000	Active TSS	Fetal Kidney	kidney
45	chr17:46124600-46129600	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr17:46124800-46126400	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr17:46124800-46126400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr17:46124800-46126400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr17:46124800-46126400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr17:46124800-46126400	Active TSS	Fetal Lung	lung

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