Variant report

Variant	rs28879694
Chromosome Location	chr7:64145824-64145825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:64145454-64145883	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:64144467-64147798	GM12891	blood:	n/a	n/a
3	POLR2A	chr7:64145588-64146129	GM12891	blood:	n/a	n/a
4	POLR2A	chr7:64145654-64145850	Hela-S3	cervix:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:64144942..64146734-chr7:64146825..64148804,2	MCF-7	breast:
2	chr7:64138840..64143249-chr7:64144344..64147303,3	K562	blood:
3	chr7:64125080..64128959-chr7:64143328..64147169,6	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF138-3	chr7:64144713-64147263	NONHSAT121038
2	lnc-ZNF138-3	chr7:64144713-64148208	NR_104148
3	lnc-ZNF138-3	chr7:64144713-64148208	NR_104149

No data

Variant related genes	Relation type
ZNF107	TF binding region
ENSG00000196247	Chromatin interaction
ENSG00000271550	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10085367	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10247618	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10248287	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253381	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10273013	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766737	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11769008	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11972903	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11974709	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11980700	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17779736	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28537641	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2862794	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34676383	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3750027	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750029	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56955205	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58101050	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460176	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6460178	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66509430	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6944545	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6944849	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6946200	0.86[EUR][1000 genomes]
rs6949440	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6955970	0.87[EUR][1000 genomes]
rs6963252	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6966466	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969837	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970764	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6973333	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6973346	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975253	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975404	0.84[EUR][1000 genomes]
rs73136779	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136786	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136802	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138703	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138715	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7782515	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7802372	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804972	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9791622	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422405	chr7:63709739-64632341	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv427787	chr7:63741770-64419520	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv2764000	chr7:63766980-64275251	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription 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 miRNA	33 gene(s)	inside rSNPs	diseases
4	esv2755057	chr7:63819849-64345822	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
5	nsv1031703	chr7:63839601-64225952	Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
6	nsv464518	chr7:63881238-64506904	Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv607312	chr7:63881238-64506904	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv888271	chr7:63961212-64295884	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv888273	chr7:63990100-64291622	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
10	nsv888274	chr7:63990100-64331123	Strong transcription ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
11	nsv888275	chr7:63990100-64468590	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv888276	chr7:63990100-64511564	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
13	nsv1021893	chr7:63995601-64155027	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
14	nsv538892	chr7:63995601-64155027	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
15	esv16290	chr7:64058602-64162829	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
16	nsv888279	chr7:64094285-64331123	Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
17	nsv970856	chr7:64126256-64155821	Strong transcription Active TSS ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs28879694	ZNF107	Cis_1M	lymphoblastoid	RTeQTL
rs28879694	ZNF107	cis	Skin Sun Exposed Lower leg	GTEx
rs28879694	RP11-561N12.7	cis	Skin Sun Exposed Lower leg	GTEx
rs28879694	ZNF138	cis	Skin Sun Exposed Lower leg	GTEx
rs28879694	ZNF107	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:64127200-64146000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr7:64127400-64153600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr7:64128200-64167600	Weak transcription	Hela-S3	cervix
4	chr7:64128200-64168000	Weak transcription	Brain Angular Gyrus	brain
5	chr7:64128800-64168000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr7:64132000-64146800	Weak transcription	Psoas Muscle	Psoas
7	chr7:64138400-64152600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
8	chr7:64138600-64147400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
9	chr7:64138600-64153000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
10	chr7:64138600-64162200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr7:64138600-64168400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:64138800-64147800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
13	chr7:64138800-64153000	ZNF genes & repeats	GM12878-XiMat	blood
14	chr7:64139000-64149000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:64139200-64147000	ZNF genes & repeats	Fetal Brain Male	brain
16	chr7:64139200-64147400	ZNF genes & repeats	Primary B cells from cord blood	blood
17	chr7:64139400-64146600	ZNF genes & repeats	Primary T cells from cord blood	blood
18	chr7:64139400-64146600	ZNF genes & repeats	Fetal Muscle Leg	muscle
19	chr7:64139400-64147000	ZNF genes & repeats	Fetal Stomach	stomach
20	chr7:64139400-64147400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
21	chr7:64139400-64147400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
22	chr7:64139400-64148000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:64139400-64148000	ZNF genes & repeats	Fetal Intestine Small	intestine
24	chr7:64139400-64148000	ZNF genes & repeats	Thymus	Thymus
25	chr7:64139400-64148600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:64139400-64148600	ZNF genes & repeats	Brain Germinal Matrix	brain
27	chr7:64139400-64153000	ZNF genes & repeats	Fetal Brain Female	brain
28	chr7:64139400-64155000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr7:64139600-64146000	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr7:64139600-64146200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr7:64139600-64147400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
32	chr7:64139600-64148000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr7:64139600-64148000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr7:64139600-64149000	ZNF genes & repeats	Fetal Thymus	thymus
35	chr7:64139800-64146000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
36	chr7:64139800-64146000	Strong transcription	HepG2	liver
37	chr7:64139800-64146200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr7:64139800-64146400	ZNF genes & repeats	Lung	lung
39	chr7:64139800-64146600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr7:64139800-64146600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr7:64139800-64146600	Strong transcription	Brain Anterior Caudate	brain
42	chr7:64139800-64148000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
43	chr7:64140000-64146400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr7:64140200-64147600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr7:64140800-64146800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:64140800-64146800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr7:64140800-64147400	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:64140800-64148000	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr7:64140800-64148600	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:64141000-64148000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links