Variant report

Variant	rs34440977
Chromosome Location	chr7:100180060-100180061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HDAC2	chr7:100179696-100180522	MCF-7	breast:	n/a	n/a
2	POLR2A	chr7:100177235-100180963	HepG2	liver:	n/a	n/a
3	EP300	chr7:100179834-100180232	T-47D	breast:	n/a	n/a
4	GATA3	chr7:100179672-100180493	MCF-7	breast:	n/a	n/a
5	NR2F2	chr7:100179530-100180731	MCF-7	breast:	n/a	n/a
6	MAX	chr7:100179541-100180502	MCF-7	breast:	n/a	n/a
7	MAX	chr7:100179502-100180360	MCF-7	breast:	n/a	n/a
8	POLR2A	chr7:100179784-100180383	K562	blood:	n/a	n/a
9	NR2F2	chr7:100179593-100180522	MCF-7	breast:	n/a	n/a
10	MYC	chr7:100179774-100180083	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:100179326..100185857-chr7:100269460..100275597,19	MCF-7	breast:
2	chr7:100031924..100034212-chr7:100179842..100183716,3	MCF-7	breast:
3	chr7:100070743..100075629-chr7:100178965..100183270,7	K562	blood:
4	chr7:100179385..100182357-chr7:100273234..100275046,2	K562	blood:
5	chr7:100179244..100181643-chr7:100480633..100482895,2	MCF-7	breast:
6	chr7:100178369..100186125-chr7:100269651..100278553,26	MCF-7	breast:

No data

Variant related genes	Relation type
LRCH4	TF binding region
FBXO24	TF binding region
ENSG00000087087	Chromatin interaction
ENSG00000240211	Chromatin interaction
ENSG00000241357	Chromatin interaction
ENSG00000160813	Chromatin interaction
ENSG00000172354	Chromatin interaction
ENSG00000166925	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11972116	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11977607	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978096	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978967	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12154919	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216707	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406243	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56307653	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58509206	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60668677	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60743967	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61309832	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61318457	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67147615	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67535650	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970240	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154884	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154887	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154891	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154894	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154895	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154897	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154902	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156207	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156210	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156211	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711133	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711136	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73711137	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784759	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799695	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888776	chr7:100014711-100198386	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	297 gene(s)	inside rSNPs	diseases
3	nsv888777	chr7:100014711-100221867	Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
4	nsv888778	chr7:100014711-100236593	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	310 gene(s)	inside rSNPs	diseases
5	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
6	nsv888780	chr7:100032665-100198386	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	nsv888782	chr7:100064719-100236593	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
8	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
9	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
10	nsv888788	chr7:100161557-100186066	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	52 gene(s)	inside rSNPs	diseases
11	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
12	nsv5868	chr7:100169998-100214646	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	59 gene(s)	inside rSNPs	diseases
13	nsv607932	chr7:100172495-100182691	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
14	esv3380438	chr7:100176116-100180514	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs34440977	SAP25	cis	Esophagus Muscularis	GTEx
rs34440977	LRCH4	cis	Esophagus Muscularis	GTEx
rs34440977	SERPINE1	cis	lymphoblastoid	seeQTL
rs34440977	SAP25	cis	Thyroid	GTEx
rs34440977	SAP25	cis	Nerve Tibial	GTEx
rs34440977	SAP25	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100169600-100180200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr7:100170000-100181200	Weak transcription	Hela-S3	cervix
3	chr7:100170200-100180200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:100170200-100180200	Strong transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:100170200-100180800	Strong transcription	Brain Germinal Matrix	brain
6	chr7:100170400-100180200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr7:100170600-100180800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr7:100171000-100180200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:100171000-100180600	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr7:100171400-100180600	Strong transcription	Fetal Brain Female	brain
11	chr7:100171600-100180400	Strong transcription	Brain Inferior Temporal Lobe	brain
12	chr7:100171600-100180400	Strong transcription	Brain Substantia Nigra	brain
13	chr7:100171600-100180800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:100171600-100181400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:100171600-100181600	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr7:100171800-100180200	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr7:100171800-100180200	Strong transcription	Left Ventricle	heart
18	chr7:100171800-100180400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:100172000-100180400	Strong transcription	Brain Anterior Caudate	brain
20	chr7:100172200-100180200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr7:100172200-100180800	Strong transcription	Brain Hippocampus Middle	brain
22	chr7:100172400-100180200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr7:100172600-100180200	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr7:100172600-100180400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr7:100172800-100180200	Strong transcription	Colon Smooth Muscle	Colon
26	chr7:100172800-100180200	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr7:100173200-100180200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr7:100173400-100180200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:100173600-100180400	Strong transcription	HSMM	muscle
30	chr7:100174400-100181600	Weak transcription	Psoas Muscle	Psoas
31	chr7:100175200-100180400	Strong transcription	Osteobl	bone
32	chr7:100175400-100180200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:100175400-100180200	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr7:100176600-100180400	Strong transcription	Right Ventricle	heart
35	chr7:100177400-100180200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:100177400-100180200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr7:100177400-100180400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr7:100177400-100180400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
39	chr7:100177400-100180800	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr7:100177600-100180200	Strong transcription	HMEC	breast
41	chr7:100177600-100180200	Strong transcription	HUVEC	blood vessel
42	chr7:100177800-100180200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr7:100178000-100180200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr7:100178200-100180200	Genic enhancers	Primary T cells from cord blood	blood
45	chr7:100178200-100180200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
46	chr7:100178200-100180400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr7:100178200-100180800	Genic enhancers	Pancreas	Pancrea
48	chr7:100178400-100180800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr7:100178600-100180400	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr7:100178600-100180600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links