Variant report

Variant	rs7528331
Chromosome Location	chr1:228641393-228641394
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	POLR2A	chr1:228639909-228642215	K562	blood:	n/a	n/a
2	POLR2A	chr1:228639678-228642181	Hela-S3	cervix:	n/a	n/a
3	JUN	chr1:228639464-228641509	K562	blood:	n/a	chr1:228640231-228640241 chr1:228640230-228640242 chr1:228640231-228640241 chr1:228640054-228640062 chr1:228640231-228640241 chr1:228640232-228640240
4	POLR2A	chr1:228641313-228641729	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:228640087-228642351	K562	blood:	n/a	n/a
6	POLR2A	chr1:228639922-228642237	H1-hESC	embryonic stem cell:	n/a	n/a
7	IRF1	chr1:228640971-228641441	K562	blood:	n/a	chr1:228641155-228641172 chr1:228641160-228641173 chr1:228641165-228641178 chr1:228641159-228641179 chr1:228641166-228641178 chr1:228641161-228641178 chr1:228641166-228641177 chr1:228641160-228641173 chr1:228641159-228641172 chr1:228641161-228641175 chr1:228641163-228641177 chr1:228641153-228641173 chr1:228641160-228641173 chr1:228641160-228641171 chr1:228641158-228641172 chr1:228641160-228641174 chr1:228641385-228641394 chr1:228641164-228641178
8	POLR2A	chr1:228639912-228642257	H1-hESC	embryonic stem cell:	n/a	n/a
9	CEBPD	chr1:228639953-228642416	K562	blood:	n/a	n/a
10	BCLAF1	chr1:228640187-228642462	K562	blood:	n/a	chr1:228641384-228641393
11	CHD2	chr1:228641216-228641609	K562	blood:	n/a	n/a
12	HEY1	chr1:228641232-228642351	K562	blood:	n/a	n/a
13	POLR2A	chr1:228639970-228646628	K562	blood:	n/a	n/a
14	POLR2A	chr1:228639400-228643883	K562	blood:	n/a	n/a
15	POLR2A	chr1:228639520-228642480	K562	blood:	n/a	n/a
16	POLR2A	chr1:228639995-228642169	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228638761..228647671-chr1:228695176..228704605,18	K562	blood:
2	chr1:228589639..228603795-chr1:228638211..228648676,43	MCF-7	breast:
3	chr1:228561337..228563891-chr1:228640710..228642796,2	MCF-7	breast:
4	chr1:228527085..228530281-chr1:228640175..228642076,3	K562	blood:
5	chr1:228352277..228353871-chr1:228640997..228643857,2	K562	blood:
6	chr1:228616675..228619300-chr1:228638219..228642365,5	MCF-7	breast:
7	chr1:228640213..228643182-chr1:228687753..228691528,4	K562	blood:
8	chr1:228462628..228466791-chr1:228639657..228643732,4	K562	blood:
9	chr1:228565749..228568495-chr1:228638648..228642089,3	K562	blood:
10	chr1:228275073..228277944-chr1:228639266..228642188,2	K562	blood:

Variant related genes	Relation type
HIST3H2BB	TF binding region
ENSG00000230841	TF binding region
ENSG00000162931	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000231563	Chromatin interaction
ENSG00000154370	Chromatin interaction
ENSG00000154358	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000215811	Chromatin interaction
ENSG00000269934	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10916315	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916316	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10916318	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes]
rs10916319	1.00[EUR][1000 genomes]
rs11808955	0.85[LWK][hapmap]
rs12091870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16841344	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs16848618	0.89[EUR][1000 genomes]
rs2104436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291998	0.89[EUR][1000 genomes]
rs34297060	0.89[EUR][1000 genomes]
rs3738688	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs4653550	0.89[EUR][1000 genomes]
rs4653952	0.89[EUR][1000 genomes]
rs4653953	0.89[EUR][1000 genomes]
rs4653957	0.89[EUR][1000 genomes]
rs4653958	0.89[EUR][1000 genomes]
rs4653961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653963	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56721656	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56895565	0.89[EUR][1000 genomes]
rs58110358	0.89[EUR][1000 genomes]
rs59225017	0.89[EUR][1000 genomes]
rs60640636	0.89[EUR][1000 genomes]
rs6679518	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6690116	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511681	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
9	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
10	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv873281	chr1:228505739-228656780	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
12	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
13	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
14	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228634000-228643200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:228634200-228641600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:228634200-228643000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:228634200-228644800	Weak transcription	Gastric	stomach
5	chr1:228634400-228641600	Weak transcription	Brain Angular Gyrus	brain
6	chr1:228634400-228644200	Weak transcription	Brain Anterior Caudate	brain
7	chr1:228634400-228644600	Weak transcription	Right Atrium	heart
8	chr1:228634400-228644600	Weak transcription	Right Ventricle	heart
9	chr1:228635000-228641400	Weak transcription	Brain Germinal Matrix	brain
10	chr1:228635000-228641600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:228635000-228642000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:228635200-228643000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:228635200-228644200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:228635600-228641400	Weak transcription	Fetal Brain Female	brain
15	chr1:228635800-228643000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:228637000-228641600	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:228637400-228643000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:228637600-228643400	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:228638000-228643000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:228638200-228643200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:228638400-228643400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:228638400-228644600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:228638800-228644600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:228639000-228643200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:228639200-228641400	Strong transcription	Fetal Intestine Small	intestine
26	chr1:228639600-228642000	Enhancers	K562	blood
27	chr1:228639600-228642200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:228639800-228641800	Enhancers	Spleen	Spleen
29	chr1:228639800-228642200	Enhancers	A549	lung
30	chr1:228640000-228641600	Genic enhancers	Placenta	Placenta
31	chr1:228640000-228643000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:228640000-228643400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:228640000-228644000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:228640200-228641400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:228640200-228643000	Strong transcription	Fetal Stomach	stomach
36	chr1:228640200-228644200	Weak transcription	Fetal Kidney	kidney
37	chr1:228640400-228641600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:228640400-228644800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:228640600-228641400	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr1:228640600-228641800	Weak transcription	HMEC	breast
41	chr1:228640600-228642200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:228640600-228643400	Weak transcription	NHDF-Ad	bronchial
43	chr1:228640600-228644200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:228640600-228644800	Weak transcription	Esophagus	oesophagus
45	chr1:228640800-228643200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:228640800-228643600	Weak transcription	NHLF	lung
47	chr1:228641000-228641600	Enhancers	GM12878-XiMat	blood
48	chr1:228641000-228642400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:228641000-228642400	Enhancers	HepG2	liver
50	chr1:228641000-228644600	Weak transcription	Fetal Muscle Trunk	muscle

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