Variant report

Variant	rs10187060
Chromosome Location	chr2:190305786-190305787
allele	C/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	SIN3AK20	chr2:190305476-190306675	MCF-7	breast:	n/a	n/a
2	MYC	chr2:190305429-190306855	MCF10A-Er-Src	breast:	n/a	chr2:190305871-190305880 chr2:190305868-190305881 chr2:190305868-190305881 chr2:190305868-190305881 chr2:190305870-190305879 chr2:190305870-190305879 chr2:190305865-190305884 chr2:190305869-190305880 chr2:190305870-190305879 chr2:190305869-190305880
3	ELF1	chr2:190305372-190306496	MCF-7	breast:	n/a	n/a
4	POLR2A	chr2:190305468-190306611	MCF-7	breast:	n/a	n/a
5	POU2F2	chr2:190305566-190306569	GM12891	blood:	n/a	n/a
6	TAF1	chr2:190305375-190306704	A549	lung:	n/a	n/a
7	SRF	chr2:190305614-190305938	GM12878	blood:	n/a	n/a
8	TBP	chr2:190305367-190306645	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr2:190305412-190306670	K562	blood:	n/a	n/a
10	MAX	chr2:190305320-190306737	HepG2	liver:	n/a	chr2:190305871-190305880 chr2:190305868-190305881 chr2:190305868-190305881 chr2:190305868-190305881 chr2:190305870-190305879 chr2:190305870-190305879 chr2:190305865-190305884 chr2:190305869-190305880 chr2:190305870-190305879 chr2:190305869-190305880
11	TAF1	chr2:190305419-190306557	SK-N-SH	brain:	n/a	n/a
12	MYC	chr2:190305449-190306888	NB4	blood:	n/a	chr2:190305871-190305880 chr2:190305868-190305881 chr2:190305868-190305881 chr2:190305868-190305881 chr2:190305870-190305879 chr2:190305870-190305879 chr2:190305865-190305884 chr2:190305869-190305880 chr2:190305870-190305879 chr2:190305869-190305880
13	JUND	chr2:190305553-190306545	H1-hESC	embryonic stem cell:	n/a	n/a
14	RELA	chr2:190305372-190306866	GM12891	blood:	n/a	n/a
15	GTF2F1	chr2:190305594-190306484	H1-hESC	embryonic stem cell:	n/a	n/a
16	YY1	chr2:190305600-190306537	K562	blood:	n/a	n/a
17	SRF	chr2:190305653-190305939	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:190305432-190306727	GM12892	blood:	n/a	n/a
19	TAF1	chr2:190305560-190306492	MCF-7	breast:	n/a	n/a
20	NFIC	chr2:190305485-190306411	GM12878	blood:	n/a	n/a
21	YY1	chr2:190305441-190306541	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr2:190305582-190306584	A549	lung:	n/a	chr2:190305871-190305880 chr2:190305868-190305881 chr2:190305868-190305881 chr2:190305868-190305881 chr2:190305870-190305879 chr2:190305870-190305879 chr2:190305865-190305884 chr2:190305869-190305880 chr2:190305870-190305879 chr2:190305869-190305880
23	SP4	chr2:190305472-190306481	H1-hESC	embryonic stem cell:	n/a	chr2:190306331-190306347
24	MAZ	chr2:190305464-190306554	Hela-S3	cervix:	n/a	chr2:190305871-190305880 chr2:190305868-190305881 chr2:190305868-190305881 chr2:190305868-190305881 chr2:190305870-190305879 chr2:190305870-190305879 chr2:190305865-190305884 chr2:190305869-190305880 chr2:190305870-190305879 chr2:190305869-190305880
25	POLR2A	chr2:190305364-190306537	IMR90	lung:	n/a	n/a
26	MAX	chr2:190305413-190306686	MCF-7	breast:	n/a	chr2:190305871-190305880 chr2:190305868-190305881 chr2:190305868-190305881 chr2:190305868-190305881 chr2:190305870-190305879 chr2:190305870-190305879 chr2:190305865-190305884 chr2:190305869-190305880 chr2:190305870-190305879 chr2:190305869-190305880
27	USF1	chr2:190305636-190306390	HepG2	liver:	n/a	n/a
28	CREB1	chr2:190305458-190306450	H1-hESC	embryonic stem cell:	n/a	n/a
29	TCF12	chr2:190305396-190306596	ECC-1	luminal epithelium:	n/a	n/a
30	TBL1XR1	chr2:190305578-190306404	K562	blood:	n/a	n/a
31	POLR2A	chr2:190305432-190305975	GM12878	blood:	n/a	n/a
32	HEY1	chr2:190305466-190306764	HepG2	liver:	n/a	n/a
33	YY1	chr2:190305539-190305980	HCT-116	colon:	n/a	n/a
34	FOS	chr2:190305687-190305962	MCF10A-Er-Src	breast:	n/a	n/a
35	USF1	chr2:190305708-190306317	HepG2	liver:	n/a	n/a
36	ATF2	chr2:190305461-190306260	H1-hESC	embryonic stem cell:	n/a	n/a
37	TAF1	chr2:190305482-190306471	GM12891	blood:	n/a	n/a
38	GTF2F1	chr2:190305670-190306406	K562	blood:	n/a	n/a
39	RCOR1	chr2:190305502-190306696	GM12878	blood:	n/a	n/a
40	CEBPD	chr2:190305453-190305930	HepG2	liver:	n/a	n/a
41	POLR2A	chr2:190305549-190306423	HepG2	liver:	n/a	n/a
42	POLR2A	chr2:190305308-190306575	K562	blood:	n/a	n/a
43	MAX	chr2:190305635-190306483	H1-hESC	embryonic stem cell:	n/a	chr2:190305871-190305880 chr2:190305868-190305881 chr2:190305868-190305881 chr2:190305868-190305881 chr2:190305870-190305879 chr2:190305870-190305879 chr2:190305865-190305884 chr2:190305869-190305880 chr2:190305870-190305879 chr2:190305869-190305880
44	BHLHE40	chr2:190305630-190306482	HepG2	liver:	n/a	n/a
45	ZC3H11A	chr2:190305492-190306124	K562	blood:	n/a	n/a
46	ELF1	chr2:190305482-190306303	A549	lung:	n/a	n/a
47	TAF1	chr2:190305243-190306728	H1-neurons	neurons:	n/a	n/a
48	CTCF	chr2:190305740-190305890	HCFaa	heart:	n/a	n/a
49	SRF	chr2:190305336-190306548	HCT-116	colon:	n/a	chr2:190306333-190306343
50	POLR2A	chr2:190305135-190306667	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:189957671..189960669-chr2:190305441..190307362,2	K562	blood:
2	chr2:190305660..190307734-chr2:190445889..190448100,2	K562	blood:
3	chr1:32110020..32110843-chr2:190305648..190306645,2	Hela-S3	cervix:
4	chr2:190305631..190306174-chr21:36260951..36261609,2	NB4	blood:
5	chr2:190304707..190307490-chr2:190326258..190329056,2	MCF-7	breast:
6	chr2:190303322..190305954-chr2:190450812..190452876,2	K562	blood:
7	chr1:149222351..149224556-chr2:190304141..190305936,2	MCF-7	breast:
8	chr2:190044174..190048765-chr2:190304090..190306138,4	MCF-7	breast:
9	chr2:190305610..190306129-chr8:101963956..101964734,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC40A1-1	chr2:190305749-190305807	XLOC_002433
2	lnc-SLC40A1-1	chr2:190305749-190305828	XLOC_002433

Variant related genes	Relation type
WDR75	TF binding region
ENSG00000204262	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000228073	Chromatin interaction
ENSG00000115368	Chromatin interaction
ENSG00000138449	Chromatin interaction
ENSG00000162517	Chromatin interaction
ENSG00000235790	Chromatin interaction
ENSG00000159216	Chromatin interaction
ENSG00000264078	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10497700	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10497703	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10755004	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10931416	0.89[ASN][1000 genomes]
rs10931418	0.90[ASN][1000 genomes]
rs10931419	0.90[ASN][1000 genomes]
rs1112578	0.89[ASN][1000 genomes]
rs1157910	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11677066	0.89[ASN][1000 genomes]
rs11688021	0.90[ASN][1000 genomes]
rs11691691	0.84[ASN][1000 genomes]
rs11695159	0.91[ASN][1000 genomes]
rs12612412	0.91[ASN][1000 genomes]
rs12613876	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs12616234	0.89[ASN][1000 genomes]
rs12623723	0.90[ASN][1000 genomes]
rs12987962	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12988143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12990035	0.88[ASN][1000 genomes]
rs12990235	0.89[ASN][1000 genomes]
rs12997620	0.90[ASN][1000 genomes]
rs13010531	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13015203	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13032853	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13033841	0.90[ASN][1000 genomes]
rs1402368	0.90[ASN][1000 genomes]
rs1520855	0.91[ASN][1000 genomes]
rs1520857	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[ASN][1000 genomes]
rs1520864	0.89[ASN][1000 genomes]
rs1581351	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2119069	0.85[ASN][1000 genomes]
rs2304703	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35997606	0.85[ASN][1000 genomes]
rs4287797	0.90[ASN][1000 genomes]
rs4667281	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6434339	0.85[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap]
rs6728055	0.90[ASN][1000 genomes]
rs6745108	0.90[ASN][1000 genomes]
rs7419276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7576165	0.84[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap]
rs7588453	0.89[ASN][1000 genomes]
rs7593821	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7596592	0.90[ASN][1000 genomes]
rs963738	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9679659	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv584062	chr2:190272195-190376493	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190304600-190307200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:190304800-190307400	Active TSS	K562	blood
3	chr2:190305000-190306200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr2:190305000-190306600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:190305000-190306600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:190305000-190306800	Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr2:190305000-190306800	Active TSS	Brain Germinal Matrix	brain
8	chr2:190305000-190306800	Active TSS	Duodenum Mucosa	Duodenum
9	chr2:190305000-190306800	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr2:190305000-190306800	Active TSS	Fetal Muscle Leg	muscle
11	chr2:190305000-190306800	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr2:190305000-190307000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:190305000-190307000	Active TSS	Fetal Intestine Large	intestine
14	chr2:190305000-190307000	Active TSS	HSMMtube	muscle
15	chr2:190305000-190307200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:190305000-190307200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:190305000-190307200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:190305000-190307200	Active TSS	Psoas Muscle	Psoas
19	chr2:190305000-190307200	Active TSS	Right Atrium	heart
20	chr2:190305000-190307200	Active TSS	A549	lung
21	chr2:190305000-190307400	Active TSS	H1 Cell Line	embryonic stem cell
22	chr2:190305000-190307400	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr2:190305000-190307400	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr2:190305000-190307400	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr2:190305000-190307400	Active TSS	Fetal Brain Female	brain
26	chr2:190305000-190307400	Active TSS	HMEC	breast
27	chr2:190305000-190307600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr2:190305000-190307600	Active TSS	Stomach Smooth Muscle	stomach
29	chr2:190305000-190307800	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr2:190305000-190307800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:190305000-190307800	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr2:190305000-190307800	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr2:190305000-190307800	Active TSS	NHLF	lung
34	chr2:190305000-190308200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:190305200-190305800	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr2:190305200-190306200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:190305200-190306600	Active TSS	Primary B cells from peripheral blood	blood
38	chr2:190305200-190306600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:190305200-190306600	Active TSS	Colon Smooth Muscle	Colon
40	chr2:190305200-190306800	Active TSS	Primary T cells fromperipheralblood	blood
41	chr2:190305200-190306800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr2:190305200-190306800	Active TSS	Fetal Brain Male	brain
43	chr2:190305200-190306800	Active TSS	Fetal Intestine Small	intestine
44	chr2:190305200-190306800	Active TSS	Thymus	Thymus
45	chr2:190305200-190306800	Active TSS	NHDF-Ad	bronchial
46	chr2:190305200-190307000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:190305200-190307000	Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr2:190305200-190307000	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr2:190305200-190307000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:190305200-190307000	Active TSS	Colonic Mucosa	Colon

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