Variant report

Variant	rs11247975
Chromosome Location	chr4:1165130-1165131
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:1165120-1165270	GM12878	blood:	n/a	n/a
2	CTCF	chr4:1165120-1165270	HPAF	blood vessel:	n/a	n/a
3	GABPA	chr4:1165036-1165380	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr4:1165080-1165177	Spleen_OC	spleen:	n/a	n/a
5	MAX	chr4:1164982-1165306	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr4:1165020-1165170	GM12870	blood:	n/a	n/a
7	CTCF	chr4:1165060-1165210	GM12875	blood:	n/a	n/a
8	POLR2A	chr4:1159180-1166648	PFSK-1	brain:	n/a	n/a
9	CTCF	chr4:1165056-1165499	GM19238	blood:	n/a	n/a
10	CHD2	chr4:1165091-1165309	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr4:1165080-1165230	AG09319	gingival:	n/a	n/a
12	MXI1	chr4:1165120-1165267	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr4:1165070-1165454	GM12891	blood:	n/a	n/a
14	CTCF	chr4:1165100-1165250	GM12867	blood:	n/a	n/a
15	CTCF	chr4:1165088-1165277	GM19239	blood:	n/a	n/a
16	MAX	chr4:1164649-1165475	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr4:1164636-1165477	H1-hESC	embryonic stem cell:	n/a	n/a
18	E2F6	chr4:1164540-1165835	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr4:1165126-1165316	GM10248	blood:	n/a	n/a
20	CTCF	chr4:1165080-1165230	AG04449	skin:	n/a	n/a
21	CTCF	chr4:1165094-1165265	GM19240	blood:	n/a	n/a
22	POLR2A	chr4:1165041-1165790	PFSK-1	brain:	n/a	n/a
23	CTCF	chr4:1165120-1165270	SAEC	small airway:	n/a	n/a
24	E2F6	chr4:1164627-1165447	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr4:1165000-1165250	GM12868	blood:	n/a	n/a
26	CTCF	chr4:1165072-1165260	NHEK	skin:	n/a	n/a
27	CTCF	chr4:1165120-1165270	GM12864	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:1161114..1165211-chr4:1166165..1170804,4	MCF-7	breast:
2	chr4:1160924..1165328-chr4:1340425..1343058,5	MCF-7	breast:
3	chr4:1160471..1164177-chr4:1164804..1166602,3	K562	blood:

No data

Variant related genes	Relation type
SPON2	TF binding region
ENSG00000163945	Chromatin interaction
ENSG00000273179	Chromatin interaction
ENSG00000159674	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12505896	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13132174	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17164229	0.90[CHB][hapmap];0.89[CHD][hapmap]
rs17164235	0.90[CHB][hapmap]
rs2127908	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2279279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28569895	0.82[ASN][1000 genomes]
rs35637542	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4368552	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974562	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4974563	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4974564	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4974591	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974627	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4974629	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62296477	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6826705	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs750305	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7659624	0.85[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs878323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs963598	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv536980	chr4:827866-1167377	Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv1009619	chr4:901897-1215657	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1003876	chr4:927509-1191316	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1000381	chr4:927509-1198766	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
8	nsv1005990	chr4:1015652-1167619	Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv1012892	chr4:1086871-1176630	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
12	nsv878329	chr4:1147407-1254930	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
14	nsv519106	chr4:1158991-1174861	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv593276	chr4:1159680-1227469	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
16	nsv461151	chr4:1159680-1236840	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
17	nsv593277	chr4:1159680-1236840	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	nsv878331	chr4:1159680-1254930	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
19	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
20	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11247975	CRIPAK	cis	lymphoblastoid	seeQTL
rs11247975	CRIPAK	cis	parietal	SCAN
rs11247975	RNF212	cis	cerebellum	SCAN
rs11247975	KIAA1530	cis	parietal	SCAN
rs11247975	RNF212	cis	Esophagus Muscularis	GTEx
rs11247975	RNF212	cis	parietal	SCAN
rs11247975	MFSD10	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1161800-1165200	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:1162000-1165200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr4:1162000-1165200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:1162000-1165200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr4:1162000-1166200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:1162600-1165200	Genic enhancers	Esophagus	oesophagus
7	chr4:1163000-1165200	ZNF genes & repeats	Spleen	Spleen
8	chr4:1163400-1165800	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:1163600-1165200	Genic enhancers	Liver	Liver
10	chr4:1164000-1165200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
11	chr4:1164000-1166000	Transcr. at gene 5' and 3'	NHLF	lung
12	chr4:1164000-1167000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
13	chr4:1164200-1165200	Bivalent Enhancer	Fetal Intestine Small	intestine
14	chr4:1164200-1165200	Bivalent Enhancer	Placenta	Placenta
15	chr4:1164200-1165400	Weak transcription	HepG2	liver
16	chr4:1164200-1165600	Enhancers	Pancreas	Pancrea
17	chr4:1164200-1166400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:1164200-1167200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
19	chr4:1164400-1165200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:1164400-1165800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:1164400-1166200	Bivalent Enhancer	Fetal Brain Male	brain
22	chr4:1164400-1167200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
23	chr4:1164600-1165200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
24	chr4:1164600-1165200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
25	chr4:1164600-1165200	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr4:1164600-1165200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:1164600-1165200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr4:1164600-1165200	Bivalent Enhancer	Fetal Thymus	thymus
29	chr4:1164600-1165200	Enhancers	Lung	lung
30	chr4:1164600-1165600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
31	chr4:1164600-1165600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
32	chr4:1164600-1165600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
33	chr4:1164600-1165600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
34	chr4:1164600-1165800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr4:1164600-1166200	Flanking Active TSS	Right Ventricle	heart
36	chr4:1164600-1166400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:1164600-1166400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
38	chr4:1164600-1166600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
39	chr4:1164600-1166600	Bivalent/Poised TSS	Fetal Brain Female	brain
40	chr4:1164600-1166600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
41	chr4:1164600-1166800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:1164800-1165200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
43	chr4:1164800-1165200	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:1164800-1165200	Bivalent/Poised TSS	Primary T helper cells fromperipheralblood	blood
45	chr4:1164800-1165200	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:1164800-1165200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr4:1164800-1165200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
48	chr4:1164800-1165200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
49	chr4:1164800-1165200	Bivalent Enhancer	Left Ventricle	heart
50	chr4:1164800-1165400	Active TSS	Primary T cells from cord blood	blood

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