Variant report

Variant	rs7512012
Chromosome Location	chr1:161162173-161162174
allele	A/G
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	CTCF	chr1:161162040-161162190	AoAF	blood vessel:	n/a	n/a
2	CTCF	chr1:161161790-161162896	SK-N-SH	brain:	n/a	chr1:161162467-161162483 chr1:161162466-161162484
3	CTCF	chr1:161162098-161162181	GM19238	blood:	n/a	n/a
4	CTCF	chr1:161162060-161162210	SK-N-SH_RA	brain:	n/a	n/a
5	RAD21	chr1:161162009-161162835	HCT-116	colon:	n/a	chr1:161162467-161162486 chr1:161162470-161162483 chr1:161162472-161162484
6	RAD21	chr1:161161897-161163099	SK-N-SH	brain:	n/a	chr1:161162467-161162486 chr1:161162470-161162483 chr1:161162472-161162484
7	REST	chr1:161162147-161163100	H1-neurons	neurons:	n/a	n/a
8	CTCF	chr1:161162088-161162193	GM19240	blood:	n/a	n/a
9	SMC3	chr1:161161869-161162893	SK-N-SH	brain:	n/a	chr1:161162468-161162482
10	SPI1	chr1:161162136-161162624	HL-60	blood:	n/a	n/a
11	CTCF	chr1:161162131-161162201	GM10266	blood:	n/a	n/a
12	CTCF	chr1:161162040-161162190	A549	lung:	n/a	n/a
13	CTCF	chr1:161162089-161162190	K562	blood:	n/a	n/a
14	CTCF	chr1:161161856-161162894	A549	lung:	n/a	chr1:161162467-161162483 chr1:161162466-161162484
15	CTCF	chr1:161162107-161162204	Spleen_OC	spleen:	n/a	n/a
16	RAD21	chr1:161162049-161162832	HCT-116	colon:	n/a	chr1:161162467-161162486 chr1:161162470-161162483 chr1:161162472-161162484
17	CTCF	chr1:161162133-161162747	HCT-116	colon:	n/a	chr1:161162467-161162483 chr1:161162466-161162484

No.	Distal block	Cell Line	Cell type
1	chr1:161157327..161160707-chr1:161160939..161164830,4	K562	blood:
2	chr1:161160904..161162773-chr1:161163879..161166104,2	MCF-7	breast:
3	chr1:161141540..161143132-chr1:161160506..161162338,2	K562	blood:
4	chr1:161161386..161164009-chr1:161188467..161191186,2	MCF-7	breast:
5	chr1:161086324..161088936-chr1:161160817..161162569,2	K562	blood:
6	chr1:161152355..161156919-chr1:161160220..161163172,6	K562	blood:
7	chr1:161162124..161162789-chr1:161260973..161261767,2	MCF-7	breast:
8	chr1:161159866..161163748-chr1:161166740..161171576,6	MCF-7	breast:
9	chr1:161160858..161163554-chr1:161335884..161337971,2	MCF-7	breast:
10	chr1:161161843..161164361-chr1:161165449..161168112,2	MCF-7	breast:
11	chr1:161162025..161162580-chr1:161351852..161352505,3	K562	blood:
12	chr1:161162001..161162966-chr1:161195045..161195904,3	MCF-7	breast:
13	chr1:161160427..161162959-chr1:161172142..161173737,2	MCF-7	breast:
14	chr1:161159836..161162629-chr1:161171704..161173335,2	MCF-7	breast:
15	chr1:161161591..161163343-chr1:161282376..161284544,2	K562	blood:

Variant related genes	Relation type
NDUFS2	TF binding region
ENSG00000143252	Chromatin interaction
ENSG00000158882	Chromatin interaction
ENSG00000235477	Chromatin interaction
ENSG00000268387	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000158859	Chromatin interaction
ENSG00000158864	Chromatin interaction
ENSG00000158850	Chromatin interaction
ENSG00000188931	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10797094	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11265564	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12024799	1.00[JPT][hapmap]
rs2501876	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2502806	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs3813622	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4073054	0.82[GIH][hapmap]
rs4233367	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4564157	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4589131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4656993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	esv32799	chr1:161161838-161171520	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7512012	B4GALT3	cis	cerebellum	SCAN
rs7512012	TAGLN2	cis	parietal	SCAN
rs7512012	DCAF8	cis	cerebellum	SCAN
rs7512012	OR10J5	cis	cerebellum	SCAN
rs7512012	FCRL3	cis	parietal	SCAN
rs7512012	NES	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161147800-161167600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:161148200-161162400	Weak transcription	Liver	Liver
3	chr1:161148200-161162600	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:161148200-161167400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:161148400-161165000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:161153200-161166000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:161153200-161167000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:161156000-161162400	Weak transcription	Brain Germinal Matrix	brain
9	chr1:161156000-161167600	Weak transcription	Fetal Heart	heart
10	chr1:161156200-161163000	Weak transcription	Thymus	Thymus
11	chr1:161156200-161163200	Weak transcription	NHDF-Ad	bronchial
12	chr1:161156200-161166200	Weak transcription	Fetal Lung	lung
13	chr1:161156400-161163600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:161156400-161166000	Weak transcription	Esophagus	oesophagus
15	chr1:161156600-161165200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:161157000-161162400	Weak transcription	Fetal Brain Female	brain
17	chr1:161157400-161162600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr1:161157400-161162600	Weak transcription	HepG2	liver
19	chr1:161157600-161162600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:161157600-161164400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:161157600-161165000	Weak transcription	Right Atrium	heart
22	chr1:161157600-161167600	Weak transcription	Small Intestine	intestine
23	chr1:161157800-161162400	Weak transcription	GM12878-XiMat	blood
24	chr1:161158800-161166000	Weak transcription	Pancreas	Pancrea
25	chr1:161159200-161162200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr1:161159600-161162200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:161159600-161162200	Weak transcription	HUVEC	blood vessel
28	chr1:161159600-161162400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:161159600-161162400	Strong transcription	Fetal Stomach	stomach
30	chr1:161160200-161163000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:161160200-161163800	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr1:161160200-161167000	Enhancers	Primary B cells from peripheral blood	blood
33	chr1:161160200-161167400	Enhancers	Primary T cells fromperipheralblood	blood
34	chr1:161160400-161162200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:161160400-161162600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:161160400-161162600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:161160400-161162600	Strong transcription	Osteobl	bone
38	chr1:161160400-161164000	Strong transcription	NHLF	lung
39	chr1:161160400-161164400	Genic enhancers	Brain Hippocampus Middle	brain
40	chr1:161160400-161165400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr1:161160600-161162600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:161160600-161163000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr1:161160600-161164000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:161160600-161165800	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr1:161160800-161166800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:161161000-161162200	Weak transcription	Primary B cells from cord blood	blood
47	chr1:161161000-161162400	Weak transcription	Fetal Thymus	thymus
48	chr1:161161000-161162600	Strong transcription	Fetal Muscle Trunk	muscle
49	chr1:161161000-161162800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:161161000-161163400	Genic enhancers	Brain Cingulate Gyrus	brain

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