Variant report

Variant	rs16859050
Chromosome Location	chr2:171784896-171784897
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	HEY1	chr2:171784521-171787271	HepG2	liver:	n/a	n/a
2	MYBL2	chr2:171784465-171787362	HepG2	liver:	n/a	n/a
3	E2F6	chr2:171784861-171786347	Hela-S3	cervix:	n/a	chr2:171785475-171785486 chr2:171785524-171785535 chr2:171785524-171785535 chr2:171785528-171785535 chr2:171785524-171785535 chr2:171785738-171785748
4	MYC	chr2:171784606-171786203	NB4	blood:	n/a	n/a
5	CBX3	chr2:171784386-171786033	K562	blood:	n/a	n/a
6	ELF1	chr2:171784652-171785044	K562	blood:	n/a	chr2:171784757-171784770 chr2:171784816-171784829
7	FOXA2	chr2:171784662-171785074	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:171784731-171787309	GM12892	blood:	n/a	n/a
9	KAP1	chr2:171784681-171785820	U2OS	brain:	n/a	n/a
10	FOS	chr2:171784649-171785609	MCF10A-Er-Src	breast:	n/a	n/a
11	SPI1	chr2:171784445-171785176	HL-60	blood:	n/a	n/a
12	MXI1	chr2:171784891-171787490	GM12878	blood:	n/a	n/a
13	MYC	chr2:171784801-171785931	H1-hESC	embryonic stem cell:	n/a	n/a
14	HA-E2F1	chr2:171784742-171787123	MCF-7	breast:	n/a	chr2:171785524-171785535 chr2:171785524-171785535 chr2:171785528-171785535 chr2:171785524-171785535 chr2:171785524-171785535 chr2:171785738-171785748
15	EP300	chr2:171784758-171785956	HepG2	liver:	n/a	chr2:171785610-171785626 chr2:171785186-171785200 chr2:171784907-171784921
16	MYBL2	chr2:171784460-171787158	HepG2	liver:	n/a	n/a
17	CEBPB	chr2:171784797-171785640	GM12878	blood:	n/a	chr2:171784906-171784917 chr2:171784906-171784919
18	CHD2	chr2:171784653-171786451	Hela-S3	cervix:	n/a	n/a
19	TAF7	chr2:171784861-171786503	H1-hESC	embryonic stem cell:	n/a	n/a
20	RCOR1	chr2:171784736-171787326	K562	blood:	n/a	n/a
21	POLR2A	chr2:171784856-171788097	IMR90	lung:	n/a	n/a
22	BRCA1	chr2:171784814-171784984	GM12878	blood:	n/a	n/a
23	CHD2	chr2:171784838-171786894	HepG2	liver:	n/a	n/a
24	SPI1	chr2:171784597-171784899	GM12878	blood:	n/a	n/a
25	MTA3	chr2:171784570-171787349	GM12878	blood:	n/a	n/a
26	POLR2A	chr2:171784480-171786213	HL-60	blood:	n/a	n/a
27	POU2F2	chr2:171784774-171785988	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:171784578-171786117	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr2:171784618-171786602	HL-60	blood:	n/a	n/a
30	POLR2A	chr2:171784714-171786638	H1-hESC	embryonic stem cell:	n/a	n/a
31	CREB1	chr2:171784606-171786598	GM12878	blood:	n/a	n/a
32	MBD4	chr2:171784457-171785988	HepG2	liver:	n/a	n/a
33	ZNF143	chr2:171784775-171786050	K562	blood:	n/a	n/a
34	SPI1	chr2:171784580-171784941	GM12891	blood:	n/a	n/a
35	POLR2A	chr2:171784867-171787483	GM12878	blood:	n/a	n/a
36	STAT3	chr2:171784625-171785093	MCF10A-Er-Src	breast:	n/a	n/a
37	ELF1	chr2:171784532-171785002	A549	lung:	n/a	chr2:171784757-171784770 chr2:171784816-171784829
38	POLR2A	chr2:171784624-171786176	HepG2	liver:	n/a	n/a
39	TBP	chr2:171784666-171785739	Hela-S3	cervix:	n/a	chr2:171784697-171784708
40	NFIC	chr2:171784576-171786154	HepG2	liver:	n/a	n/a
41	FOS	chr2:171784719-171785669	MCF10A-Er-Src	breast:	n/a	n/a
42	RUNX3	chr2:171784599-171786642	GM12878	blood:	n/a	n/a
43	ELF1	chr2:171784346-171785944	MCF-7	breast:	n/a	chr2:171785740-171785749 chr2:171784757-171784770 chr2:171784816-171784829
44	POLR2A	chr2:171784748-171787066	MCF-7	breast:	n/a	n/a
45	MXI1	chr2:171784668-171787428	HepG2	liver:	n/a	n/a
46	TAF1	chr2:171784758-171785120	Hela-S3	cervix:	n/a	n/a
47	FOXA1	chr2:171784651-171784953	T-47D	breast:	n/a	n/a
48	TCF7L2	chr2:171784862-171785996	Hela-S3	cervix:	n/a	n/a
49	SMC3	chr2:171784755-171785691	HepG2	liver:	n/a	chr2:171785434-171785441 chr2:171785434-171785448 chr2:171785657-171785667 chr2:171785090-171785104
50	MBD4	chr2:171784540-171785946	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:171784604..171786258-chr2:171809996..171812623,2	MCF-7	breast:
2	chr2:171772485..171776882-chr2:171782682..171785818,4	MCF-7	breast:
3	chr2:171784510..171786977-chr2:172014779..172017241,3	K562	blood:
4	chr2:171784160..171787954-chr2:172288133..172292253,10	K562	blood:
5	chr2:171783060..171786005-chr2:216876902..216878903,2	MCF-7	breast:
6	chr2:171626961..171629009-chr2:171784250..171787377,4	K562	blood:
7	chr2:171672408..171674860-chr2:171784778..171786781,3	MCF-7	breast:
8	chr15:72765119..72766854-chr2:171784790..171787087,2	K562	blood:
9	chr2:171770723..171773648-chr2:171784124..171786319,2	K562	blood:
10	chr2:171571182..171573160-chr2:171784797..171786624,2	K562	blood:
11	chr2:171784119..171787322-chr2:172288781..172292051,4	MCF-7	breast:
12	chr2:171783791..171787349-chr2:172286549..172291928,9	K562	blood:
13	chr2:171627023..171629009-chr2:171784250..171786840,2	K562	blood:
14	chr2:171784693..171786944-chr2:172376735..172379477,2	K562	blood:
15	chr15:65596837..65597338-chr2:171784880..171785438,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TLK1-3	chr2:171784208-171785364	NONHSAT075436

Variant related genes	Relation type
GORASP2	TF binding region
ENSG00000115806	Chromatin interaction
ENSG00000166233	Chromatin interaction
ENSG00000118242	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000123600	Chromatin interaction
ENSG00000239467	Chromatin interaction
ENSG00000235934	Chromatin interaction
ENSG00000234350	Chromatin interaction
ENSG00000266020	Chromatin interaction
ENSG00000071967	Chromatin interaction
ENSG00000261423	Chromatin interaction
ENSG00000115827	Chromatin interaction
ENSG00000204335	Chromatin interaction
ENSG00000128683	Chromatin interaction
ENSG00000198586	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10198197	0.84[CEU][hapmap]
rs10208341	0.84[CEU][hapmap]
rs10210883	0.83[CEU][hapmap]
rs1025240	0.80[CEU][hapmap]
rs1035825	0.84[CEU][hapmap]
rs1035827	0.91[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs10803853	0.84[EUR][1000 genomes]
rs10803854	0.88[CEU][hapmap]
rs10930449	0.88[CEU][hapmap]
rs10930453	0.84[CEU][hapmap]
rs10930455	0.84[CEU][hapmap]
rs10930456	0.84[CEU][hapmap]
rs10930457	0.84[CEU][hapmap]
rs11686985	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11696064	0.81[CEU][hapmap];0.91[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs11902360	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11902369	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11904750	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs12467411	0.82[CHB][hapmap]
rs12473741	0.86[CHB][hapmap]
rs12477649	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap]
rs12612871	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs12618898	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12621769	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13004273	0.84[CEU][hapmap]
rs13008199	0.84[CEU][hapmap]
rs13010307	0.84[CEU][hapmap]
rs13025033	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13030784	0.84[CEU][hapmap]
rs13034529	0.84[CEU][hapmap]
rs13036123	0.81[CEU][hapmap]
rs13410683	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs13411575	0.83[CEU][hapmap]
rs13425247	0.84[CEU][hapmap]
rs1529378	0.84[CEU][hapmap]
rs1529391	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs16859157	0.82[CHB][hapmap]
rs17505447	0.86[CHB][hapmap]
rs1978592	0.84[CEU][hapmap]
rs2033160	0.81[CEU][hapmap]
rs2059723	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs2081715	0.84[CEU][hapmap]
rs2081767	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs2081768	0.86[CHB][hapmap]
rs2098999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2195116	0.96[CEU][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs2356422	0.86[CHB][hapmap]
rs2555922	0.83[CEU][hapmap]
rs2557794	0.84[CEU][hapmap]
rs2676131	0.81[CEU][hapmap]
rs2676151	0.84[CEU][hapmap]
rs2723241	0.80[CEU][hapmap]
rs3731993	0.82[CHB][hapmap]
rs3755121	0.84[CEU][hapmap]
rs3755124	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755126	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770423	0.84[CEU][hapmap]
rs3770428	0.84[CEU][hapmap]
rs3770433	0.84[CEU][hapmap]
rs3770436	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs3770438	0.91[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4667667	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667673	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4668343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668344	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668345	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668346	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668354	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4668355	0.88[CEU][hapmap]
rs4668368	0.81[CEU][hapmap]
rs5028603	0.81[CEU][hapmap]
rs6433264	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6433266	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433267	0.83[EUR][1000 genomes]
rs6433276	0.84[CEU][hapmap]
rs6729847	0.82[EUR][1000 genomes]
rs6730417	0.84[CEU][hapmap]
rs6731774	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6733178	0.83[CEU][hapmap]
rs6742564	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6742797	0.88[CEU][hapmap]
rs6754315	0.85[CEU][hapmap]
rs6760293	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6761642	0.84[CEU][hapmap]
rs731693	0.88[CEU][hapmap]
rs754058	0.82[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap]
rs7559136	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560889	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7567927	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580629	0.81[CEU][hapmap]
rs7585607	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593193	0.81[CEU][hapmap]
rs7598194	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606822	0.82[CEU][hapmap]
rs930035	0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap]
rs930036	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap]
rs964172	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431801	chr2:171721493-171966493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16859050	SP5	cis	cerebellum	SCAN
rs16859050	GORASP2	cis	cerebellum	SCAN
rs16859050	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171778400-171785000	Weak transcription	Right Atrium	heart
2	chr2:171783800-171785200	Flanking Active TSS	Dnd41	blood
3	chr2:171784400-171785000	Flanking Active TSS	A549	lung
4	chr2:171784400-171785200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:171784400-171785200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr2:171784400-171785200	Flanking Active TSS	HMEC	breast
7	chr2:171784400-171785400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr2:171784400-171787000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr2:171784400-171787600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr2:171784600-171785000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:171784600-171785000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr2:171784600-171785000	Enhancers	Primary B cells from peripheral blood	blood
13	chr2:171784600-171785000	Enhancers	Primary T cells from cord blood	blood
14	chr2:171784600-171785000	Enhancers	Primary T cells fromperipheralblood	blood
15	chr2:171784600-171785000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr2:171784600-171785000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr2:171784600-171785000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr2:171784600-171785000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:171784600-171785000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:171784600-171785000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:171784600-171785000	Enhancers	Fetal Muscle Leg	muscle
22	chr2:171784600-171785000	Enhancers	Placenta	Placenta
23	chr2:171784600-171785200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr2:171784600-171785200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr2:171784600-171785200	Flanking Active TSS	Liver	Liver
26	chr2:171784600-171785200	Enhancers	Placenta Amnion	Placenta Amnion
27	chr2:171784600-171785200	Flanking Active TSS	GM12878-XiMat	blood
28	chr2:171784600-171785400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr2:171784600-171785400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:171784600-171785400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr2:171784600-171785400	Flanking Active TSS	Hela-S3	cervix
32	chr2:171784600-171785400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr2:171784800-171785000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:171784800-171785000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:171784800-171785000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:171784800-171785000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr2:171784800-171785000	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr2:171784800-171785000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:171784800-171785000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr2:171784800-171785000	Active TSS	Fetal Intestine Small	intestine
41	chr2:171784800-171785000	Enhancers	Fetal Stomach	stomach
42	chr2:171784800-171785000	Enhancers	Fetal Thymus	thymus
43	chr2:171784800-171785000	Enhancers	Gastric	stomach
44	chr2:171784800-171785000	Enhancers	Small Intestine	intestine
45	chr2:171784800-171785000	Enhancers	Thymus	Thymus
46	chr2:171784800-171785000	Enhancers	Spleen	Spleen
47	chr2:171784800-171785000	Flanking Bivalent TSS/Enh	HepG2	liver
48	chr2:171784800-171785000	Enhancers	HSMMtube	muscle
49	chr2:171784800-171785200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
50	chr2:171784800-171785200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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