Variant report

Variant	rs10198652
Chromosome Location	chr2:55538976-55538977
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	FOS	chr2:55538578-55539060	MCF10A-Er-Src	breast:	n/a	chr2:55538840-55538851
2	EBF1	chr2:55538405-55539303	GM12878	blood:	n/a	n/a
3	CTCF	chr2:55538880-55539030	NHDF-neo	bronchial:	n/a	n/a
4	POU2F2	chr2:55538516-55539051	GM12878	blood:	n/a	n/a
5	CTCF	chr2:55538691-55539060	GM12878	blood:	n/a	n/a
6	E2F4	chr2:55538706-55539029	MCF10A-Er-Src	breast:	n/a	n/a
7	EP300	chr2:55538552-55539238	GM12878	blood:	n/a	n/a
8	PBX3	chr2:55538509-55539086	SK-N-SH	brain:	n/a	n/a
9	RUNX3	chr2:55538401-55539070	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:55538805-55539001	GM12878	blood:	n/a	n/a
11	CTCF	chr2:55538840-55538990	AG09309	skin:	n/a	n/a
12	ZNF143	chr2:55538690-55539025	GM12878	blood:	n/a	n/a
13	BATF	chr2:55538455-55539013	GM12878	blood:	n/a	n/a
14	PML	chr2:55538314-55539187	GM12878	blood:	n/a	n/a
15	RUNX3	chr2:55538195-55539113	GM12878	blood:	n/a	n/a
16	MEF2C	chr2:55538469-55539111	GM12878	blood:	n/a	chr2:55538774-55538789
17	BCL3	chr2:55538496-55539033	GM12878	blood:	n/a	n/a
18	IRF4	chr2:55538474-55539072	GM12878	blood:	n/a	n/a
19	BHLHE40	chr2:55538500-55539062	GM12878	blood:	n/a	n/a
20	RAD21	chr2:55538755-55538984	SK-N-SH_RA	brain:	n/a	n/a
21	FOS	chr2:55538578-55539038	MCF10A-Er-Src	breast:	n/a	chr2:55538840-55538851
22	STAT5A	chr2:55538471-55539070	GM12878	blood:	n/a	chr2:55538841-55538850 chr2:55538842-55538851
23	CTCF	chr2:55538860-55539010	WERI-Rb-1	eye:	n/a	n/a
24	MTA3	chr2:55538368-55539069	GM12878	blood:	n/a	n/a
25	CREB1	chr2:55538359-55539061	GM12878	blood:	n/a	n/a
26	CTCF	chr2:55538709-55539053	IMR90	lung:	n/a	n/a
27	CTCF	chr2:55538960-55539110	WI-38	lung:	n/a	n/a
28	JUND	chr2:55538747-55539022	K562	blood:	n/a	chr2:55538840-55538851
29	TCF12	chr2:55538406-55539140	SK-N-SH	brain:	n/a	n/a
30	FOSL2	chr2:55538511-55539081	SK-N-SH	brain:	n/a	n/a
31	MTA3	chr2:55538330-55539096	GM12878	blood:	n/a	n/a
32	FOXM1	chr2:55538357-55539171	GM12878	blood:	n/a	n/a
33	MEF2A	chr2:55538384-55538976	GM12878	blood:	n/a	n/a
34	EBF1	chr2:55538560-55539020	GM12878	blood:	n/a	n/a
35	BCL11A	chr2:55538417-55539027	GM12878	blood:	n/a	n/a
36	JUND	chr2:55538703-55539038	Hela-S3	cervix:	n/a	chr2:55538840-55538851
37	BCL11A	chr2:55538483-55539067	GM12878	blood:	n/a	n/a
38	RAD21	chr2:55538739-55538992	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr2:55538880-55539030	HEEpiC	esophagus:	n/a	n/a
40	EP300	chr2:55538496-55539040	SK-N-SH_RA	brain:	n/a	n/a
41	CTCF	chr2:55538840-55538990	Hela-S3	cervix:	n/a	n/a
42	NFATC1	chr2:55538378-55539035	GM12878	blood:	n/a	n/a
43	ATF2	chr2:55538284-55539073	GM12878	blood:	n/a	n/a
44	BCLAF1	chr2:55538437-55539096	GM12878	blood:	n/a	n/a
45	CTCF	chr2:55538840-55538990	GM12865	blood:	n/a	n/a
46	RAD21	chr2:55538636-55539021	GM12878	blood:	n/a	n/a
47	CTCF	chr2:55538840-55538990	GM12864	blood:	n/a	n/a
48	CEBPB	chr2:55538706-55539014	A549	lung:	n/a	n/a
49	BATF	chr2:55538437-55539121	GM12878	blood:	n/a	n/a
50	CTCF	chr2:55538793-55539021	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55536648..55539597-chr2:55541310..55544144,3	K562	blood:

Variant related genes	Relation type
ENSG00000240401	TF binding region
CCDC88A	TF binding region
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10182704	0.82[ASN][1000 genomes]
rs10184756	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10454144	0.80[ASN][1000 genomes]
rs11125563	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs11125565	0.80[ASN][1000 genomes]
rs11125566	0.81[ASN][1000 genomes]
rs11125568	0.83[CHB][hapmap]
rs12617891	0.89[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs12618795	0.83[CHB][hapmap]
rs1545554	0.89[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs1902056	0.94[CHB][hapmap];1.00[YRI][hapmap]
rs1902057	0.94[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs2043713	1.00[ASW][hapmap];0.80[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2045132	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs2576688	1.00[ASW][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2576703	0.89[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs2589057	0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs2589068	0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs2589069	0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs2589070	0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2589078	0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2589079	0.85[ASN][1000 genomes]
rs2589104	0.83[ASN][1000 genomes]
rs2864831	0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2864832	0.84[ASN][1000 genomes]
rs2867178	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs2902857	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs2903509	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs2917777	0.89[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs2920963	0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2920970	0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2920973	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2966466	0.89[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs3099080	0.89[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs3099081	0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs3099083	0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4233960	0.89[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4233961	1.00[ASW][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap]
rs4484068	1.00[CEU][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4672032	0.83[CHB][hapmap]
rs4672035	0.83[CHB][hapmap]
rs59634508	0.84[ASN][1000 genomes]
rs61157332	0.84[ASN][1000 genomes]
rs6710192	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs6718031	0.82[ASN][1000 genomes]
rs6718909	0.81[ASN][1000 genomes]
rs6721593	1.00[YRI][hapmap]
rs6724840	0.82[CHB][hapmap]
rs6725968	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs6738970	0.91[CEU][hapmap]
rs72924907	0.82[ASN][1000 genomes]
rs7557555	0.80[ASN][1000 genomes]
rs7559987	0.83[CHB][hapmap]
rs7586440	0.83[CHB][hapmap]
rs7589279	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs7601588	0.89[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs7606361	0.89[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874158	chr2:55513738-55619923	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv457941	chr2:55517491-55585915	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv582030	chr2:55517491-55585915	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10198652	FLJ31438	cis	multi-tissue	Pritchard
rs10198652	ACYP2	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55509000-55541200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55509400-55545200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:55510000-55541600	Weak transcription	Esophagus	oesophagus
4	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:55510200-55542200	Weak transcription	Fetal Intestine Large	intestine
7	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
8	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
9	chr2:55510800-55542200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:55511000-55540600	Weak transcription	Spleen	Spleen
11	chr2:55511200-55542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:55511200-55547000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:55512000-55549800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:55512400-55577400	Weak transcription	Right Ventricle	heart
15	chr2:55512600-55546000	Weak transcription	Small Intestine	intestine
16	chr2:55514800-55549600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:55515800-55550400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:55518600-55591400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:55519800-55579000	Weak transcription	Primary B cells from cord blood	blood
20	chr2:55520000-55541200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:55520200-55539000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:55520200-55554400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr2:55520400-55591200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr2:55521400-55591000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr2:55523000-55548000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:55523000-55584400	Weak transcription	Aorta	Aorta
27	chr2:55523200-55584800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr2:55523600-55541000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr2:55523600-55542000	Weak transcription	Fetal Brain Male	brain
30	chr2:55523600-55548000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:55523600-55600600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:55523800-55541000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr2:55524000-55541200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:55524800-55543200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr2:55524800-55549400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr2:55526400-55549600	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr2:55527000-55546400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:55527400-55539600	Weak transcription	K562	blood
39	chr2:55527400-55541000	Weak transcription	Brain Anterior Caudate	brain
40	chr2:55527600-55540000	Weak transcription	Fetal Kidney	kidney
41	chr2:55528600-55542000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:55529400-55544400	Weak transcription	Placenta	Placenta
43	chr2:55532200-55543800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:55533000-55542000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:55533000-55544000	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr2:55534200-55589400	Weak transcription	Pancreas	Pancrea
47	chr2:55534800-55544200	Strong transcription	Liver	Liver
48	chr2:55535200-55549600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:55535200-55549600	Strong transcription	Dnd41	blood
50	chr2:55535400-55540200	Weak transcription	Fetal Stomach	stomach

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