Variant report

Variant	rs3823646
Chromosome Location	chr7:99757612-99757613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99757562-99757618	K562	blood:	n/a	n/a
2	POLR2A	chr7:99757314-99758468	H1-neurons	neurons:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:2906493..2908640-chr7:99756107..99758046,2	MCF-7	breast:
2	chr7:99756435..99758861-chr7:99763048..99766609,5	K562	blood:
3	chr7:99696160..99700887-chr7:99753963..99757907,5	K562	blood:
4	chr7:99752857..99757651-chr7:99763240..99770051,14	MCF-7	breast:
5	chr7:99754180..99757947-chr7:99773944..99778293,5	K562	blood:
6	chr7:99696142..99700081-chr7:99754300..99760427,7	MCF-7	breast:
7	chr7:99726058..99730231-chr7:99754511..99757895,5	MCF-7	breast:
8	chr7:99751463..99761050-chr7:99772463..99778676,10	K562	blood:
9	chr7:99724063..99726491-chr7:99755814..99759003,3	K562	blood:
10	chr7:99756236..99758894-chr7:100025899..100028598,2	K562	blood:
11	chr7:99696160..99699295-chr7:99753963..99757907,4	K562	blood:
12	chr7:99753966..99755669-chr7:99756075..99758782,2	MCF-7	breast:
13	chr6:150037573..150039874-chr7:99755624..99757771,2	MCF-7	breast:
14	chr7:99755258..99758996-chr7:99773394..99775783,3	MCF-7	breast:

No data

Variant related genes	Relation type
C7orf43	TF binding region
MIR4658	TF binding region
ENSG00000214309	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000213420	Chromatin interaction
ENSG00000242798	Chromatin interaction
ENSG00000221838	Chromatin interaction
ENSG00000263325	Chromatin interaction
ENSG00000197093	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000066923	Chromatin interaction
ENSG00000131023	Chromatin interaction
ENSG00000005001	Chromatin interaction
ENSG00000146826	Chromatin interaction
ENSG00000166508	Chromatin interaction
ENSG00000235077	Chromatin interaction
ENSG00000266154	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10231604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11764584	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11771167	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12705070	0.85[YRI][hapmap]
rs12878	0.88[GIH][hapmap];0.88[MEX][hapmap]
rs1527423	0.89[CEU][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap]
rs1918352	0.83[EUR][1000 genomes]
rs1918353	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs2272337	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2405440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34130487	0.82[AFR][1000 genomes]
rs35042434	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3736590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736591	0.88[GIH][hapmap];0.83[MEX][hapmap];0.80[ASN][1000 genomes]
rs3779047	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3800951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4424195	0.85[YRI][hapmap]
rs7785392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7787294	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7787492	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7807641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs999885	0.85[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
2	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
3	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
4	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
5	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
6	nsv427794	chr7:99750981-99960900	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv428180	chr7:99750981-99960900	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv888773	chr7:99751594-99772298	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv971181	chr7:99757433-99769748	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3823646	ZSCAN21	cis	parietal	SCAN
rs3823646	AP4M1	cis	Artery Tibial	GTEx
rs3823646	ZKSCAN1	cis	multi-tissue	Pritchard
rs3823646	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs3823646	AP4M1	cis	multi-tissue	Pritchard
rs3823646	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs3823646	TAF6	cis	Thyroid	GTEx
rs3823646	AP4M1	cis	cerebellum	SCAN
rs3823646	AP4M1	cis	lymphoblastoid	seeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99755600-99758400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:99756600-99760400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:99756600-99764200	Weak transcription	Spleen	Spleen
4	chr7:99756800-99758000	Enhancers	Primary T cells fromperipheralblood	blood
5	chr7:99756800-99758200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:99756800-99758200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr7:99756800-99758600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr7:99756800-99758600	Enhancers	Placenta	Placenta
9	chr7:99756800-99760600	Weak transcription	Colonic Mucosa	Colon
10	chr7:99756800-99760600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr7:99756800-99760800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:99756800-99764200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:99756800-99765200	Weak transcription	Right Atrium	heart
14	chr7:99756800-99765400	Weak transcription	Pancreas	Pancrea
15	chr7:99757000-99759000	Enhancers	K562	blood
16	chr7:99757000-99759400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:99757000-99759800	Weak transcription	Fetal Intestine Large	intestine
18	chr7:99757000-99760400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr7:99757000-99760400	Weak transcription	Fetal Intestine Small	intestine
20	chr7:99757000-99760400	Weak transcription	NHEK	skin
21	chr7:99757000-99760600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr7:99757000-99760600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr7:99757000-99760600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr7:99757000-99760600	Weak transcription	Primary B cells from cord blood	blood
25	chr7:99757000-99760600	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr7:99757000-99760600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr7:99757000-99760600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr7:99757000-99760600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr7:99757000-99760600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr7:99757000-99760600	Weak transcription	Stomach Mucosa	stomach
31	chr7:99757000-99760600	Weak transcription	A549	lung
32	chr7:99757000-99760600	Weak transcription	GM12878-XiMat	blood
33	chr7:99757000-99761000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr7:99757000-99763800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr7:99757000-99763800	Weak transcription	Fetal Brain Female	brain
36	chr7:99757000-99764000	Weak transcription	Brain Hippocampus Middle	brain
37	chr7:99757000-99764000	Weak transcription	Fetal Lung	lung
38	chr7:99757000-99764600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr7:99757000-99764600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr7:99757000-99765000	Weak transcription	HSMM	muscle
41	chr7:99757000-99765400	Weak transcription	HSMMtube	muscle
42	chr7:99757200-99759200	Strong transcription	Fetal Thymus	thymus
43	chr7:99757200-99759600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr7:99757200-99759600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:99757200-99759800	Weak transcription	Primary T cells from cord blood	blood
46	chr7:99757200-99760400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr7:99757200-99760400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr7:99757200-99760400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr7:99757200-99760400	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr7:99757200-99760400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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