Variant report

Variant	rs17332742
Chromosome Location	chr2:231276234-231276235
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:90)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:90 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:231276231-231276903	Hela-S3	cervix:	n/a	n/a
2	STAT1	chr2:231276089-231276885	GM12878	blood:	n/a	chr2:231276625-231276636
3	POLR2A	chr2:231275889-231276994	GM19099	blood:	n/a	n/a
4	POLR2A	chr2:231276157-231276981	U87	brain:	n/a	n/a
5	POLR2A	chr2:231276169-231277041	GM12878	blood:	n/a	n/a
6	MAX	chr2:231275762-231277128	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:231276187-231277060	GM12892	blood:	n/a	n/a
8	PML	chr2:231275893-231277239	GM12878	blood:	n/a	n/a
9	CHD2	chr2:231276136-231277122	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr2:231276157-231276950	U87	brain:	n/a	n/a
11	POLR2A	chr2:231276234-231276972	Hela-S3	cervix:	n/a	n/a
12	UBTF	chr2:231276223-231277086	K562	blood:	n/a	n/a
13	POLR2A	chr2:231276018-231276241	HUVEC	blood vessel:	n/a	n/a
14	HEY1	chr2:231276204-231277033	HepG2	liver:	n/a	n/a
15	MYC	chr2:231276177-231277032	NB4	blood:	n/a	n/a
16	POLR2A	chr2:231276165-231276982	HepG2	liver:	n/a	n/a
17	POLR2A	chr2:231276124-231276977	GM12892	blood:	n/a	n/a
18	JUN	chr2:231276191-231276380	K562	blood:	n/a	n/a
19	NFIC	chr2:231276043-231276999	HepG2	liver:	n/a	n/a
20	CTCF	chr2:231276220-231276370	AG04450	lung:	n/a	n/a
21	ELF1	chr2:231275676-231276566	GM12878	blood:	n/a	n/a
22	MTA3	chr2:231275706-231276706	GM12878	blood:	n/a	n/a
23	MAX	chr2:231276213-231277036	HCT-116	colon:	n/a	n/a
24	POLR2A	chr2:231276175-231277088	GM15510	blood:	n/a	n/a
25	POLR2A	chr2:231276006-231277108	U87	brain:	n/a	n/a
26	MAX	chr2:231276109-231277167	A549	lung:	n/a	n/a
27	POLR2A	chr2:231276145-231276960	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr2:231275956-231277189	GM12892	blood:	n/a	n/a
29	POLR2A	chr2:231276082-231276980	SK-N-SH	brain:	n/a	n/a
30	RAD21	chr2:231276068-231276758	IMR90	lung:	n/a	n/a
31	POLR2A	chr2:231276222-231276930	IMR90	lung:	n/a	n/a
32	POLR2A	chr2:231275724-231277160	GM12892	blood:	n/a	n/a
33	POLR2A	chr2:231276189-231277062	GM12878	blood:	n/a	n/a
34	RUNX3	chr2:231276183-231276898	GM12878	blood:	n/a	n/a
35	CTCF	chr2:231276180-231276330	GM12873	blood:	n/a	n/a
36	POLR2A	chr2:231276073-231277284	GM19193	blood:	n/a	n/a
37	POLR2A	chr2:231276123-231277357	NB4	blood:	n/a	n/a
38	HNF4G	chr2:231276223-231276818	HepG2	liver:	n/a	chr2:231276397-231276419
39	POLR2A	chr2:231276218-231276944	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr2:231276168-231277039	GM18505	blood:	n/a	n/a
41	POLR2A	chr2:231276148-231277095	K562	blood:	n/a	n/a
42	POLR2A	chr2:231275981-231277193	HepG2	liver:	n/a	n/a
43	TAF1	chr2:231276233-231277006	HepG2	liver:	n/a	n/a
44	POLR2A	chr2:231275626-231277125	GM12878	blood:	n/a	n/a
45	GATA1	chr2:231276225-231276885	PBDE	blood:	n/a	chr2:231276601-231276617
46	POLR2A	chr2:231276045-231277287	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr2:231276124-231277068	GM18951	blood:	n/a	n/a
48	MAX	chr2:231276000-231276948	NB4	blood:	n/a	n/a
49	MAZ	chr2:231276144-231276863	K562	blood:	n/a	n/a
50	MAX	chr2:231275879-231277192	HepG2	liver:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:231187646..231188478-chr2:231276184..231277085,2	HCT-116	colon:
2	chr2:231269734..231271710-chr2:231274995..231278115,3	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP110-6	chr2:231275415-231277244	NONHSAT077283

No data

Variant related genes	Relation type
SP100	TF binding region

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1074886	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11675127	0.94[ASN][1000 genomes]
rs11675135	0.94[ASN][1000 genomes]
rs11676089	0.94[ASN][1000 genomes]
rs11676310	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11677462	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11677512	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11677646	0.91[ASN][1000 genomes]
rs11679026	0.91[ASN][1000 genomes]
rs11681234	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11681358	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11687964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11688362	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11688458	0.87[ASN][1000 genomes]
rs11692506	1.00[JPT][hapmap]
rs11692527	0.94[ASN][1000 genomes]
rs11692602	0.94[ASN][1000 genomes]
rs11693767	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11694346	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694422	0.90[ASN][1000 genomes]
rs11694428	0.90[ASN][1000 genomes]
rs11695277	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12694865	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1427284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17273079	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17332171	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17333189	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2303608	0.93[ASN][1000 genomes]
rs35919859	0.90[ASN][1000 genomes]
rs3752431	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs3754940	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3754941	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3754942	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3754943	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3769849	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3815885	0.93[ASN][1000 genomes]
rs3893836	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs55637456	0.87[ASN][1000 genomes]
rs55770359	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55893188	0.91[ASN][1000 genomes]
rs55964110	0.94[ASN][1000 genomes]
rs56007282	0.93[ASN][1000 genomes]
rs56044062	0.94[ASN][1000 genomes]
rs56052963	0.94[ASN][1000 genomes]
rs56105857	0.94[ASN][1000 genomes]
rs56108366	0.94[ASN][1000 genomes]
rs56251216	0.94[ASN][1000 genomes]
rs56270546	0.85[ASN][1000 genomes]
rs56303947	0.94[ASN][1000 genomes]
rs56372741	0.87[ASN][1000 genomes]
rs56401027	0.91[ASN][1000 genomes]
rs6436933	0.94[ASN][1000 genomes]
rs6706167	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6713447	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6713465	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6722656	0.90[ASN][1000 genomes]
rs6725726	0.90[ASN][1000 genomes]
rs6732684	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6732940	0.94[ASN][1000 genomes]
rs6748339	0.94[ASN][1000 genomes]
rs6748445	0.94[ASN][1000 genomes]
rs6750712	0.93[ASN][1000 genomes]
rs6753500	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6759292	0.93[ASN][1000 genomes]
rs6761255	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs68096532	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72495174	0.94[ASN][1000 genomes]
rs72495175	0.94[ASN][1000 genomes]
rs72495176	0.94[ASN][1000 genomes]
rs72495180	0.94[ASN][1000 genomes]
rs72495181	0.94[ASN][1000 genomes]
rs72495182	0.94[ASN][1000 genomes]
rs72495183	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72495185	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs725202	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs72994332	0.91[ASN][1000 genomes]
rs72996270	0.91[ASN][1000 genomes]
rs72996292	0.94[ASN][1000 genomes]
rs72998203	0.94[ASN][1000 genomes]
rs72998264	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72998283	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73000239	0.93[ASN][1000 genomes]
rs73000253	0.93[ASN][1000 genomes]
rs73000268	0.93[ASN][1000 genomes]
rs7559665	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7563909	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7565654	0.81[ASN][1000 genomes]
rs7568128	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585646	0.94[ASN][1000 genomes]
rs7585731	0.94[ASN][1000 genomes]
rs7589948	0.94[ASN][1000 genomes]
rs7597033	0.94[ASN][1000 genomes]
rs7606804	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999888	1.00[JPT][hapmap];0.87[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	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2751844	chr2:231179495-231280495	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv875946	chr2:231184106-231277567	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv875947	chr2:231190446-231281286	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv521344	chr2:231267925-231281286	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv584671	chr2:231273229-231284556	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17332742	SP140L	cis	Nerve Tibial	GTEx
rs17332742	LOC93349	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231275200-231276400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr2:231275400-231276400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:231275600-231276400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr2:231275600-231276400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:231275600-231276400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:231275600-231276400	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr2:231275600-231276400	Flanking Active TSS	Duodenum Mucosa	Duodenum
8	chr2:231275600-231276400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
9	chr2:231275600-231276400	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr2:231275600-231276400	Flanking Active TSS	Osteobl	bone
11	chr2:231275600-231277000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:231275600-231277200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr2:231275600-231277400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:231275800-231276400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:231275800-231276400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr2:231275800-231276400	Flanking Active TSS	Primary B cells from peripheral blood	blood
17	chr2:231275800-231276400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr2:231275800-231276400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:231275800-231276400	Flanking Active TSS	Liver	Liver
20	chr2:231275800-231276400	Flanking Active TSS	Fetal Muscle Leg	muscle
21	chr2:231275800-231276400	Flanking Active TSS	Dnd41	blood
22	chr2:231275800-231276400	Flanking Active TSS	GM12878-XiMat	blood
23	chr2:231275800-231276400	Flanking Active TSS	HMEC	breast
24	chr2:231275800-231276400	Flanking Active TSS	NHLF	lung
25	chr2:231275800-231276800	Active TSS	NH-A	brain
26	chr2:231275800-231277000	Active TSS	Primary T cells from cord blood	blood
27	chr2:231275800-231277000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:231275800-231277200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr2:231275800-231277200	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr2:231275800-231277200	Active TSS	A549	lung
31	chr2:231276000-231276400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
32	chr2:231276000-231276400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:231276000-231276400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:231276000-231276400	Active TSS	Primary B cells from cord blood	blood
35	chr2:231276000-231276400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr2:231276000-231276400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:231276000-231276400	Flanking Active TSS	Fetal Brain Male	brain
38	chr2:231276000-231276400	Flanking Active TSS	Fetal Muscle Trunk	muscle
39	chr2:231276000-231276400	Flanking Active TSS	Placenta	Placenta
40	chr2:231276000-231276400	Flanking Active TSS	Fetal Stomach	stomach
41	chr2:231276000-231276400	Flanking Active TSS	Fetal Thymus	thymus
42	chr2:231276000-231276400	Flanking Active TSS	Thymus	Thymus
43	chr2:231276000-231276400	Flanking Active TSS	HSMMtube	muscle
44	chr2:231276000-231276400	Flanking Active TSS	HUVEC	blood vessel
45	chr2:231276000-231276400	Flanking Active TSS	K562	blood
46	chr2:231276000-231276600	Flanking Active TSS	NHEK	skin
47	chr2:231276000-231276800	Active TSS	Primary hematopoietic stem cells	blood
48	chr2:231276000-231276800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr2:231276000-231276800	Active TSS	Brain Hippocampus Middle	brain
50	chr2:231276000-231277000	Active TSS	Breast Myoepithelial Primary Cells	Breast

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