Variant report

Variant	rs6433616
Chromosome Location	chr2:177679576-177679577
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	RAD21	chr2:177679460-177679842	Hela-S3	cervix:	n/a	chr2:177679679-177679698
2	SIN3AK20	chr2:177678831-177679678	MCF-7	breast:	n/a	n/a
3	GATA2	chr2:177679436-177679741	HUVEC	blood vessel:	n/a	n/a
4	CTCF	chr2:177679537-177679790	GM12878	blood:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
5	CTCF	chr2:177679560-177679710	HFF	foreskin:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
6	CTCF	chr2:177679482-177679788	K562	blood:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
7	CTCF	chr2:177679540-177679690	GM12872	blood:	n/a	n/a
8	GATA3	chr2:177679308-177679841	SK-N-SH	brain:	n/a	n/a
9	CTCF	chr2:177679573-177679660	MCF-7	breast:	n/a	n/a
10	CTCF	chr2:177679540-177679690	BE2_C	brain:	n/a	n/a
11	CTCF	chr2:177679560-177679710	BJ	skin:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
12	ZNF143	chr2:177679542-177679756	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr2:177679465-177679878	MCF-7	breast:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
14	CTCF	chr2:177679460-177679610	HCT-116	colon:	n/a	n/a
15	RAD21	chr2:177679539-177679795	K562	blood:	n/a	chr2:177679679-177679698
16	CTCF	chr2:177679560-177679710	MCF-7	breast:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
17	RAD21	chr2:177679505-177679848	IMR90	lung:	n/a	chr2:177679679-177679698
18	RAD21	chr2:177679462-177679882	H1-hESC	embryonic stem cell:	n/a	chr2:177679679-177679698
19	RAD21	chr2:177679481-177679825	K562	blood:	n/a	chr2:177679679-177679698
20	CTCF	chr2:177679560-177679710	HEK293	kidney:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
21	RAD21	chr2:177679388-177679850	ECC-1	luminal epithelium:	n/a	chr2:177679679-177679698
22	CTCF	chr2:177679521-177679818	A549	lung:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
23	CTCF	chr2:177679560-177679710	GM12872	blood:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
24	CTCF	chr2:177679518-177679835	Spleen_OC	spleen:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
25	CTCF	chr2:177679560-177679710	GM12866	blood:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
26	CTCF	chr2:177679520-177679670	GM12867	blood:	n/a	n/a
27	CTCF	chr2:177679520-177679670	SAEC	small airway:	n/a	n/a
28	CTCF	chr2:177679540-177679690	GM12864	blood:	n/a	n/a
29	RAD21	chr2:177679395-177679853	SK-N-SH_RA	brain:	n/a	chr2:177679679-177679698
30	ZNF143	chr2:177679491-177679857	GM12878	blood:	n/a	n/a
31	RAD21	chr2:177679444-177679846	GM12878	blood:	n/a	chr2:177679679-177679698
32	CTCF	chr2:177679566-177679747	A549	lung:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
33	CTCF	chr2:177679439-177679828	A549	lung:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
34	RAD21	chr2:177679455-177679829	SK-N-SH_RA	brain:	n/a	chr2:177679679-177679698
35	CTCF	chr2:177679503-177679772	H1-hESC	embryonic stem cell:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
36	CTCF	chr2:177679493-177679862	HCT-116	colon:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
37	CTCF	chr2:177679162-177680329	A549	lung:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
38	CTCF	chr2:177679558-177679686	Gliobla	brain:	n/a	n/a
39	RAD21	chr2:177679489-177679841	GM12878	blood:	n/a	chr2:177679679-177679698
40	CTCF	chr2:177679500-177679650	WI-38	lung:	n/a	n/a
41	RAD21	chr2:177679463-177679743	HepG2	liver:	n/a	chr2:177679679-177679698
42	CTCF	chr2:177679560-177679710	HCT-116	colon:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
43	CTCF	chr2:177679560-177679710	NHEK	skin:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
44	FOXM1	chr2:177678797-177679678	MCF-7	breast:	n/a	n/a
45	CTCF	chr2:177679537-177679806	HUVEC	blood vessel:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
46	CTCF	chr2:177679564-177679759	SK-N-SH_RA	brain:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
47	CTCF	chr2:177679571-177679775	Kidney_OC	kidney:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
48	CTCF	chr2:177679560-177679710	K562	blood:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
49	CTCF	chr2:177679560-177679710	WERI-Rb-1	eye:	n/a	chr2:177679676-177679697 chr2:177679681-177679699
50	CTCF	chr2:177679560-177679710	HEEpiC	esophagus:	n/a	chr2:177679676-177679697 chr2:177679681-177679699

No.	Distal block	Cell Line	Cell type
1	chr2:177004878..177006132-chr2:177679220..177679989,4	MCF-7	breast:
2	chr2:177516751..177517622-chr2:177679221..177680084,2	MCF-7	breast:
3	chr2:177518427..177519228-chr2:177679235..177679802,3	MCF-7	breast:
4	chr2:177678711..177679684-chr2:177710502..177711032,2	MCF-7	breast:
5	chr2:177543870..177544476-chr2:177679175..177679998,2	MCF-7	breast:
6	chr2:177516771..177517762-chr2:177679104..177680158,5	MCF-7	breast:
7	chr2:177672353..177675128-chr2:177678147..177680944,2	K562	blood:
8	chr2:177610086..177610770-chr2:177679196..177679715,2	MCF-7	breast:
9	chr2:177518336..177518879-chr2:177679032..177679756,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223777	TF binding region
ENSG00000223777	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1098452	1.00[EUR][1000 genomes]
rs1153669	1.00[EUR][1000 genomes]
rs1251031	1.00[EUR][1000 genomes]
rs1251036	1.00[EUR][1000 genomes]
rs13383291	1.00[EUR][1000 genomes]
rs13400152	1.00[EUR][1000 genomes]
rs13401042	1.00[EUR][1000 genomes]
rs13415518	1.00[EUR][1000 genomes]
rs1513872	1.00[EUR][1000 genomes]
rs16864739	1.00[EUR][1000 genomes]
rs1849605	1.00[EUR][1000 genomes]
rs2203301	1.00[EUR][1000 genomes]
rs2203302	1.00[EUR][1000 genomes]
rs4893918	0.90[ASW][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs57416198	1.00[EUR][1000 genomes]
rs57736481	1.00[EUR][1000 genomes]
rs57742539	1.00[EUR][1000 genomes]
rs59784805	1.00[EUR][1000 genomes]
rs59975233	1.00[EUR][1000 genomes]
rs60505165	1.00[EUR][1000 genomes]
rs60806293	1.00[EUR][1000 genomes]
rs73039484	1.00[EUR][1000 genomes]
rs73039488	1.00[EUR][1000 genomes]
rs73039490	1.00[EUR][1000 genomes]
rs73039495	1.00[EUR][1000 genomes]
rs73041409	1.00[EUR][1000 genomes]
rs73041425	1.00[EUR][1000 genomes]
rs73041476	1.00[EUR][1000 genomes]
rs73041480	1.00[EUR][1000 genomes]
rs73041485	1.00[EUR][1000 genomes]
rs7607833	1.00[EUR][1000 genomes]
rs840680	1.00[EUR][1000 genomes]
rs840683	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs840688	1.00[EUR][1000 genomes]
rs840689	1.00[EUR][1000 genomes]
rs840690	0.80[MKK][hapmap];1.00[EUR][1000 genomes]
rs840692	1.00[EUR][1000 genomes]
rs840693	1.00[EUR][1000 genomes]
rs840694	1.00[EUR][1000 genomes]
rs840695	1.00[EUR][1000 genomes]
rs840705	1.00[EUR][1000 genomes]
rs938273	1.00[EUR][1000 genomes]
rs938274	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527737	chr2:177538266-177692572	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv583686	chr2:177538266-177692572	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006500	chr2:177548521-177707097	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:177676800-177679600	Enhancers	Fetal Lung	lung
2	chr2:177677200-177679600	Enhancers	Ovary	ovary
3	chr2:177677400-177681600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:177678000-177680200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr2:177678200-177679600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr2:177678200-177679600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr2:177678200-177679600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr2:177678200-177679600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr2:177678200-177679600	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr2:177678200-177683400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:177678400-177679600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:177678600-177681600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:177678600-177683200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:177678800-177679600	Enhancers	Liver	Liver
15	chr2:177678800-177679600	Enhancers	Rectal Smooth Muscle	rectum
16	chr2:177679000-177683400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:177679200-177679600	Enhancers	HepG2	liver
18	chr2:177679200-177680000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr2:177679400-177679600	Enhancers	H1 Cell Line	embryonic stem cell
20	chr2:177679400-177679600	Enhancers	Primary T cells from cord blood	blood
21	chr2:177679400-177679600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:177679400-177679600	Enhancers	Brain Anterior Caudate	brain
23	chr2:177679400-177679600	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:177679400-177679600	Enhancers	Brain Substantia Nigra	brain
25	chr2:177679400-177679600	Enhancers	Fetal Kidney	kidney
26	chr2:177679400-177680000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr2:177679400-177680200	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr2:177679400-177681000	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr2:177679400-177681200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:177679400-177681600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:177679400-177681600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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