Variant report

Variant	rs28429963
Chromosome Location	chr5:37251893-37251894
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	USF1	chr5:37251787-37252101	A549	lung:	n/a	chr5:37251960-37251971
2	USF1	chr5:37251803-37252077	K562	blood:	n/a	chr5:37251960-37251971
3	USF2	chr5:37251778-37252138	Hela-S3	cervix:	n/a	chr5:37251960-37251971
4	USF1	chr5:37251868-37252062	HepG2	liver:	n/a	chr5:37251960-37251971
5	USF1	chr5:37251668-37252242	HCT-116	colon:	n/a	chr5:37251960-37251971
6	TBP	chr5:37251775-37251913	K562	blood:	n/a	n/a
7	USF1	chr5:37251791-37252022	A549	lung:	n/a	chr5:37251960-37251971
8	USF1	chr5:37251767-37252175	SK-N-SH	brain:	n/a	chr5:37251960-37251971
9	USF1	chr5:37251856-37252062	A549	lung:	n/a	chr5:37251960-37251971
10	ZNF143	chr5:37251829-37252112	Hela-S3	cervix:	n/a	n/a
11	USF1	chr5:37251740-37252028	H1-hESC	embryonic stem cell:	n/a	chr5:37251960-37251971
12	ZNF143	chr5:37251797-37252003	GM12878	blood:	n/a	n/a
13	USF1	chr5:37251705-37252146	ECC-1	luminal epithelium:	n/a	chr5:37251960-37251971

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:37248573..37251161-chr5:37251715..37254222,2	MCF-7	breast:

Variant related genes	Relation type
C5orf42	TF binding region
ENSG00000197603	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10037680	0.87[AMR][1000 genomes]
rs10038960	1.00[EUR][1000 genomes]
rs10051872	1.00[CEU][hapmap]
rs10067278	1.00[CEU][hapmap]
rs10070367	1.00[CEU][hapmap]
rs10071032	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs10072236	1.00[EUR][1000 genomes]
rs10077819	1.00[CEU][hapmap]
rs10078741	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs10079237	1.00[EUR][1000 genomes]
rs10085007	0.87[AMR][1000 genomes]
rs10440646	1.00[EUR][1000 genomes]
rs10472286	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs10473042	0.96[AFR][1000 genomes]
rs10491332	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11739318	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11949393	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11949707	1.00[EUR][1000 genomes]
rs11955258	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs12109225	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs13160250	1.00[CEU][hapmap]
rs13356505	1.00[EUR][1000 genomes]
rs1554969	1.00[CEU][hapmap]
rs16903584	0.93[AMR][1000 genomes]
rs16903599	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs16903615	1.00[CEU][hapmap]
rs1833828	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2366172	1.00[CEU][hapmap]
rs28609469	1.00[EUR][1000 genomes]
rs4242249	1.00[CEU][hapmap]
rs4869431	1.00[CEU][hapmap]
rs57061844	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57402531	1.00[EUR][1000 genomes]
rs57591687	1.00[EUR][1000 genomes]
rs58701977	1.00[EUR][1000 genomes]
rs59468995	0.87[AMR][1000 genomes]
rs59713841	1.00[EUR][1000 genomes]
rs60063938	0.87[AMR][1000 genomes]
rs60605472	1.00[EUR][1000 genomes]
rs61666447	0.88[AMR][1000 genomes]
rs6451317	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6451318	1.00[CEU][hapmap]
rs6860757	1.00[CEU][hapmap]
rs6868108	1.00[CEU][hapmap]
rs6870723	0.87[AMR][1000 genomes]
rs6876447	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6878453	1.00[EUR][1000 genomes]
rs6888095	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6892443	1.00[CEU][hapmap]
rs6895753	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes]
rs6898900	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs73068464	0.87[AMR][1000 genomes]
rs7714241	0.87[AMR][1000 genomes]
rs7728794	1.00[EUR][1000 genomes]
rs7732929	1.00[CEU][hapmap]
rs7733418	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs7735454	1.00[CEU][hapmap]
rs7736469	0.87[AMR][1000 genomes]
rs9292650	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525478	chr5:36804225-37349895	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv1793961	chr5:36866835-37361728	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv530225	chr5:36886635-37331912	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1024051	chr5:36899712-37303001	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv537725	chr5:36899712-37303001	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv530226	chr5:36906377-37606367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv534064	chr5:37054962-37586210	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	nsv881511	chr5:37088627-37552852	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv597823	chr5:37111565-37430365	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
10	nsv1026554	chr5:37112133-37734859	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv537726	chr5:37112133-37734859	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv1025988	chr5:37115142-37586211	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
13	nsv537727	chr5:37115142-37586211	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
14	nsv830265	chr5:37152221-37312233	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
15	nsv530227	chr5:37157106-37571999	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
16	nsv880406	chr5:37173930-37345270	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	nsv880839	chr5:37173930-37465126	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
18	nsv948741	chr5:37179341-37582164	Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
19	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
20	nsv597824	chr5:37206621-37409579	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
21	nsv597825	chr5:37206621-37430365	Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
22	nsv881512	chr5:37239240-37364693	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
23	nsv880817	chr5:37239240-37465126	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
24	nsv881492	chr5:37239240-37543121	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
25	nsv880444	chr5:37239240-37556926	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
26	nsv1015983	chr5:37240827-37666601	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
27	nsv597826	chr5:37250700-37256578	ZNF genes & repeats Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37250200-37253400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:37250200-37257200	Weak transcription	Psoas Muscle	Psoas
3	chr5:37250200-37260000	Weak transcription	Brain Anterior Caudate	brain
4	chr5:37250400-37252000	Weak transcription	Fetal Intestine Large	intestine
5	chr5:37250400-37252000	Enhancers	Hela-S3	cervix
6	chr5:37250400-37256600	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:37250400-37257400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:37250400-37264200	Weak transcription	Brain Substantia Nigra	brain
9	chr5:37251800-37252000	Enhancers	Fetal Intestine Small	intestine
10	chr5:37251800-37252000	Enhancers	HepG2	liver
11	chr5:37251800-37252000	Enhancers	HSMMtube	muscle

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