Variant report

Variant	rs7598878
Chromosome Location	chr2:153574266-153574267
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	MBD4	chr2:153573120-153575962	HepG2	liver:	n/a	n/a
2	CTCF	chr2:153574260-153574410	HepG2	liver:	n/a	n/a
3	TAF1	chr2:153573418-153575850	A549	lung:	n/a	n/a
4	CTCF	chr2:153574220-153574370	AG09309	skin:	n/a	n/a
5	JUN	chr2:153573724-153575306	K562	blood:	n/a	chr2:153574146-153574155 chr2:153574147-153574156 chr2:153575007-153575021
6	SIN3AK20	chr2:153573674-153575785	PANC-1	pancreas:	n/a	n/a
7	SP4	chr2:153573628-153574407	H1-hESC	embryonic stem cell:	n/a	chr2:153574020-153574031
8	E2F6	chr2:153573491-153575937	K562	blood:	n/a	chr2:153575129-153575138 chr2:153575130-153575137 chr2:153575129-153575137 chr2:153575130-153575137 chr2:153575130-153575137 chr2:153575686-153575698
9	CREB1	chr2:153573391-153575649	HepG2	liver:	n/a	n/a
10	CTCF	chr2:153574120-153574270	AoAF	blood vessel:	n/a	n/a
11	STAT5A	chr2:153574091-153575561	GM12878	blood:	n/a	chr2:153574281-153574293 chr2:153574149-153574161 chr2:153574152-153574164 chr2:153574223-153574235 chr2:153574146-153574158
12	CUX1	chr2:153574130-153576035	K562	blood:	n/a	n/a
13	POU2F2	chr2:153573542-153574639	GM12891	blood:	n/a	chr2:153574285-153574297
14	TAF1	chr2:153573505-153575807	K562	blood:	n/a	n/a
15	TAF1	chr2:153573703-153574708	MCF-7	breast:	n/a	n/a
16	ATF1	chr2:153573694-153575695	K562	blood:	n/a	chr2:153573760-153573774
17	POLR2A	chr2:153572495-153576612	MCF10A-Er-Src	breast:	n/a	n/a
18	MAFK	chr2:153573797-153574283	HepG2	liver:	n/a	n/a
19	MAX	chr2:153573629-153575904	K562	blood:	n/a	n/a
20	SIN3A	chr2:153573139-153575943	H1-hESC	embryonic stem cell:	n/a	chr2:153574775-153574788
21	RELA	chr2:153573511-153575660	GM12892	blood:	n/a	n/a
22	TAF1	chr2:153573339-153575837	ECC-1	luminal epithelium:	n/a	n/a
23	MAX	chr2:153573380-153575816	Hela-S3	cervix:	n/a	chr2:153573447-153573457
24	JUND	chr2:153573361-153575603	GM12878	blood:	n/a	chr2:153574146-153574155 chr2:153574147-153574156 chr2:153575007-153575021
25	PML	chr2:153573188-153576331	K562	blood:	n/a	n/a
26	CEBPD	chr2:153573797-153574358	HepG2	liver:	n/a	n/a
27	POLR2A	chr2:153573694-153575723	HepG2	liver:	n/a	n/a
28	RELA	chr2:153573462-153575836	GM10847	blood:	n/a	n/a
29	POLR2A	chr2:153573585-153575693	A549	lung:	n/a	n/a
30	MAX	chr2:153573419-153575873	MCF-7	breast:	n/a	chr2:153573447-153573457
31	GABPA	chr2:153573605-153574342	A549	lung:	n/a	n/a
32	POLR2A	chr2:153573348-153575507	H1-neurons	neurons:	n/a	n/a
33	CEBPB	chr2:153574041-153575173	GM12878	blood:	n/a	n/a
34	EP300	chr2:153574041-153575208	A549	lung:	n/a	n/a
35	RELA	chr2:153573379-153576078	GM12891	blood:	n/a	n/a
36	CTCF	chr2:153574080-153574370	HEEpiC	esophagus:	n/a	n/a
37	POLR2A	chr2:153573583-153576096	GM18526	blood:	n/a	n/a
38	TAF1	chr2:153573568-153574862	K562	blood:	n/a	n/a
39	MYC	chr2:153573497-153575298	MCF-7	breast:	n/a	n/a
40	FOXP2	chr2:153573721-153575451	PFSK-1	brain:	n/a	n/a
41	TAF1	chr2:153574063-153574524	PFSK-1	brain:	n/a	n/a
42	SIN3AK20	chr2:153573318-153574425	H1-hESC	embryonic stem cell:	n/a	n/a
43	HEY1	chr2:153573173-153576234	K562	blood:	n/a	chr2:153575077-153575092 chr2:153575049-153575064
44	POLR2A	chr2:153573701-153576055	HCT-116	colon:	n/a	n/a
45	TAF1	chr2:153573675-153575526	HepG2	liver:	n/a	n/a
46	JUND	chr2:153573705-153575839	MCF-7	breast:	n/a	chr2:153574146-153574155 chr2:153574147-153574156 chr2:153575007-153575021
47	BRCA1	chr2:153573997-153574290	GM12878	blood:	n/a	n/a
48	POU2F2	chr2:153573649-153575389	GM12891	blood:	n/a	chr2:153574775-153574787 chr2:153574285-153574297
49	POLR2A	chr2:153573678-153576078	U87	brain:	n/a	n/a
50	YY1	chr2:153573686-153575750	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:153572649..153576015-chr2:157196773..157199686,4	K562	blood:
2	chr2:153030659..153033731-chr2:153574261..153576507,5	MCF-7	breast:
3	chr2:153031056..153034207-chr2:153571978..153575897,4	K562	blood:
4	chr2:153574034..153574968-chr7:2559141..2559893,2	Hela-S3	cervix:
5	chr2:153005699..153008232-chr2:153573566..153575567,2	MCF-7	breast:
6	chr2:153573043..153575205-chr8:143832270..143834692,2	MCF-7	breast:
7	chr17:8076675..8077517-chr2:153574078..153575043,2	Hela-S3	cervix:
8	chr2:153030783..153033861-chr2:153572629..153575835,5	MCF-7	breast:
9	chr1:117112856..117113728-chr2:153573715..153574484,2	Hela-S3	cervix:

Variant related genes	Relation type
ARL6IP6	TF binding region
PRPF40A	TF binding region
ENSG00000115145	Chromatin interaction
ENSG00000106003	Chromatin interaction
ENSG00000153234	Chromatin interaction
ENSG00000200463	Chromatin interaction
ENSG00000197353	Chromatin interaction
ENSG00000116815	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10497113	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931279	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1135617	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676069	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694512	0.84[ASN][1000 genomes]
rs11901227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12478681	0.84[ASN][1000 genomes]
rs12693429	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs12989903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990935	1.00[CHB][hapmap]
rs12995388	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12999331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13003670	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13006652	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13014141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022436	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023779	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13023975	0.83[EUR][1000 genomes]
rs1370499	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16831440	0.83[EUR][1000 genomes]
rs16831456	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17328776	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400456	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17400938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400952	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083097	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2346551	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34199006	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34454505	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34469468	0.84[EUR][1000 genomes]
rs34619076	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34775858	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35002744	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35421285	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35754252	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35894330	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35937874	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36107565	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36122595	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811569	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4575677	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434172	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66492085	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66849546	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6728189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736003	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71417232	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71417235	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72871148	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7591590	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 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	chr2:153572000-153576400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:153572000-153576400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:153572000-153576400	Active TSS	K562	blood
4	chr2:153572200-153576400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:153572200-153576400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:153572200-153576400	Active TSS	HMEC	breast
7	chr2:153572200-153576800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr2:153572200-153577000	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:153572400-153574400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
10	chr2:153572400-153575800	Active TSS	Fetal Brain Female	brain
11	chr2:153572400-153575800	Active TSS	Hela-S3	cervix
12	chr2:153572400-153576000	Active TSS	HSMM	muscle
13	chr2:153572400-153576200	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr2:153572400-153576200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:153572400-153576400	Active TSS	H1 Cell Line	embryonic stem cell
16	chr2:153572400-153576400	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr2:153572400-153576400	Active TSS	Fetal Kidney	kidney
18	chr2:153572400-153576400	Active TSS	A549	lung
19	chr2:153572400-153576600	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr2:153572400-153576600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:153572400-153576600	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr2:153572400-153576600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:153572400-153576600	Active TSS	NHLF	lung
24	chr2:153572400-153576800	Active TSS	H9 Cell Line	embryonic stem cell
25	chr2:153572400-153576800	Active TSS	Psoas Muscle	Psoas
26	chr2:153572400-153577000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:153572400-153577000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:153572600-153575200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:153572600-153575800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:153572600-153576000	Bivalent/Poised TSS	HepG2	liver
31	chr2:153572600-153576200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr2:153572600-153576200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:153572600-153576200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:153572600-153576200	Active TSS	Fetal Muscle Trunk	muscle
35	chr2:153572600-153576200	Active TSS	Right Ventricle	heart
36	chr2:153572600-153576200	Active TSS	HSMMtube	muscle
37	chr2:153572600-153576400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:153572600-153576400	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr2:153572600-153576400	Active TSS	GM12878-XiMat	blood
40	chr2:153572800-153574800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:153572800-153575400	Active TSS	Brain Anterior Caudate	brain
42	chr2:153572800-153575600	Active TSS	Thymus	Thymus
43	chr2:153572800-153575800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:153572800-153575800	Active TSS	Fetal Intestine Small	intestine
45	chr2:153572800-153576000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:153572800-153576000	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr2:153572800-153576000	Active TSS	Fetal Intestine Large	intestine
48	chr2:153572800-153576200	Active TSS	Fetal Muscle Leg	muscle
49	chr2:153572800-153576400	Active TSS	Fetal Stomach	stomach
50	chr2:153572800-153576400	Active TSS	Fetal Thymus	thymus

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