Variant report

Variant	rs1006002
Chromosome Location	chr4:174092588-174092589
allele	G/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	CTCF	chr4:174092314-174092618	H1-hESC	embryonic stem cell:	n/a	chr4:174092437-174092450 chr4:174092435-174092453 chr4:174092430-174092451
2	CTCF	chr4:174092440-174092590	HFF-Myc	foreskin:	n/a	n/a
3	POLR2A	chr4:174088782-174094458	PANC-1	pancreas:	n/a	n/a
4	CTCF	chr4:174092480-174092630	WI-38	lung:	n/a	n/a
5	MXI1	chr4:174092423-174092654	K562	blood:	n/a	n/a
6	ZMIZ1	chr4:174092427-174092627	K562	blood:	n/a	n/a
7	EP300	chr4:174092335-174092661	K562	blood:	n/a	chr4:174092497-174092511
8	CTCF	chr4:174091935-174092782	A549	lung:	n/a	chr4:174092437-174092450 chr4:174092435-174092453 chr4:174092430-174092451
9	RCOR1	chr4:174092531-174092731	K562	blood:	n/a	n/a
10	MYC	chr4:174092276-174092618	MCF10A-Er-Src	breast:	n/a	n/a
11	CTCF	chr4:174092290-174092615	GM12878	blood:	n/a	chr4:174092437-174092450 chr4:174092435-174092453 chr4:174092430-174092451
12	CTCF	chr4:174092480-174092630	GM12878	blood:	n/a	n/a
13	RAD21	chr4:174092275-174092617	SK-N-SH_RA	brain:	n/a	chr4:174092433-174092452
14	WRNIP1	chr4:174092442-174092817	GM12878	blood:	n/a	n/a
15	RAD21	chr4:174092220-174092642	A549	lung:	n/a	chr4:174092433-174092452
16	MYC	chr4:174092423-174092654	MCF10A-Er-Src	breast:	n/a	n/a
17	CTCF	chr4:174092460-174092610	HAc	cerebellar:	n/a	n/a
18	MXI1	chr4:174092569-174092953	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:174091835-174092963	PANC-1	pancreas:	n/a	n/a
20	RAD21	chr4:174092250-174092724	MCF-7	breast:	n/a	chr4:174092433-174092452
21	CTCF	chr4:174092440-174092590	GM12864	blood:	n/a	n/a
22	RAD21	chr4:174092285-174092661	H1-hESC	embryonic stem cell:	n/a	chr4:174092433-174092452
23	RAD21	chr4:174092242-174092645	Hela-S3	cervix:	n/a	chr4:174092433-174092452
24	CTCF	chr4:174092560-174092710	GM06990	blood:	n/a	n/a
25	CUX1	chr4:174092292-174092608	K562	blood:	n/a	n/a
26	CTCFL	chr4:174092348-174092612	K562	blood:	n/a	n/a
27	SMC3	chr4:174092340-174092685	GM12878	blood:	n/a	chr4:174092437-174092451
28	FOS	chr4:174092276-174092602	MCF10A-Er-Src	breast:	n/a	n/a
29	CTCF	chr4:174092234-174092655	A549	lung:	n/a	chr4:174092437-174092450 chr4:174092435-174092453 chr4:174092430-174092451
30	CTCF	chr4:174092213-174092901	SK-N-SH	brain:	n/a	chr4:174092437-174092450 chr4:174092435-174092453 chr4:174092430-174092451
31	CTCF	chr4:174092460-174092610	NHLF	lung:	n/a	n/a
32	CTCF	chr4:174092242-174092666	K562	blood:	n/a	chr4:174092437-174092450 chr4:174092435-174092453 chr4:174092430-174092451
33	SMC3	chr4:174092262-174092621	Hela-S3	cervix:	n/a	chr4:174092437-174092451
34	RAD21	chr4:174092265-174092589	IMR90	lung:	n/a	chr4:174092433-174092452
35	ZNF263	chr4:174088970-174092679	HEK293-T-REx	kidney:	n/a	chr4:174089685-174089706 chr4:174091315-174091324 chr4:174092434-174092443
36	CTCF	chr4:174092291-174092637	K562	blood:	n/a	chr4:174092437-174092450 chr4:174092435-174092453 chr4:174092430-174092451
37	RAD21	chr4:174092302-174092597	SK-N-SH_RA	brain:	n/a	chr4:174092433-174092452
38	CEBPB	chr4:174092340-174092620	K562	blood:	n/a	n/a
39	ZNF143	chr4:174092252-174092628	K562	blood:	n/a	n/a
40	CTCF	chr4:174092520-174092670	HVMF	connective:	n/a	n/a
41	SMC3	chr4:174092285-174092603	K562	blood:	n/a	chr4:174092437-174092451
42	JUND	chr4:174092320-174092809	K562	blood:	n/a	chr4:174092778-174092787
43	RAD21	chr4:174092269-174092637	H1-hESC	embryonic stem cell:	n/a	chr4:174092433-174092452
44	CTCF	chr4:174092272-174092621	IMR90	lung:	n/a	chr4:174092437-174092450 chr4:174092435-174092453 chr4:174092430-174092451
45	MAX	chr4:174092453-174092658	NB4	blood:	n/a	n/a
46	RCOR1	chr4:174092250-174092611	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:173946182..173946922-chr4:174091942..174093328,5	MCF-7	breast:
2	chr4:174091292..174097320-chr4:174098048..174101316,8	K562	blood:
3	chr4:173935748..173936466-chr4:174092019..174092785,2	MCF-7	breast:
4	chr4:174091423..174092924-chr4:174250225..174252885,2	K562	blood:

Variant related genes	Relation type
ENSG00000245213	TF binding region
ENSG00000248774	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10001613	0.86[TSI][hapmap]
rs10011724	0.95[ASN][1000 genomes]
rs10027708	0.88[ASN][1000 genomes]
rs10031414	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1006003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1008052	0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[ASN][1000 genomes]
rs10213525	0.80[CHB][hapmap];0.86[TSI][hapmap]
rs1054496	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1054497	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1991727	0.94[JPT][hapmap]
rs2332654	0.95[ASN][1000 genomes]
rs2332655	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2332669	0.94[JPT][hapmap]
rs28477433	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28612521	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3733477	0.96[ASN][1000 genomes]
rs4377567	0.88[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4643788	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4695826	0.93[ASN][1000 genomes]
rs6822683	0.83[ASN][1000 genomes]
rs6822875	0.83[ASN][1000 genomes]
rs6835098	0.95[ASN][1000 genomes]
rs6843769	0.84[JPT][hapmap]
rs7657374	0.81[ASN][1000 genomes]
rs7672108	0.94[JPT][hapmap]
rs9685946	0.80[TSI][hapmap]
rs9990666	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1793569	chr4:174090004-174093002	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv1793960	chr4:174090004-174102397	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1801469	chr4:174090004-174102397	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv1799519	chr4:174090004-174173743	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv1823585	chr4:174090209-174107537	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1006002	MORF4	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174091000-174092600	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr4:174091200-174094000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr4:174091400-174092800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr4:174091400-174092800	Flanking Active TSS	Dnd41	blood
5	chr4:174091400-174092800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr4:174091400-174093400	Weak transcription	Lung	lung
7	chr4:174091600-174092600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr4:174091600-174092600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr4:174091600-174092600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:174091600-174092600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:174091600-174092600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:174091600-174092600	Weak transcription	Gastric	stomach
13	chr4:174091600-174092800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr4:174091600-174092800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:174091600-174092800	Flanking Active TSS	A549	lung
16	chr4:174091600-174093000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr4:174091600-174093200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:174091600-174093200	Weak transcription	Spleen	Spleen
19	chr4:174091600-174093400	Weak transcription	Pancreas	Pancrea
20	chr4:174091600-174094200	Enhancers	Primary B cells from peripheral blood	blood
21	chr4:174091600-174094600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:174091600-174095000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:174091600-174113600	Weak transcription	Esophagus	oesophagus
24	chr4:174091800-174092600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:174091800-174092600	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr4:174091800-174092600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr4:174091800-174092600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr4:174091800-174092800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr4:174091800-174092800	Enhancers	Primary T cells from cord blood	blood
30	chr4:174091800-174092800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:174091800-174092800	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr4:174091800-174092800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr4:174091800-174092800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr4:174091800-174092800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr4:174091800-174092800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:174091800-174092800	Enhancers	Fetal Intestine Small	intestine
37	chr4:174091800-174092800	Flanking Active TSS	GM12878-XiMat	blood
38	chr4:174091800-174092800	Enhancers	HMEC	breast
39	chr4:174091800-174092800	Enhancers	NHEK	skin
40	chr4:174091800-174092800	Enhancers	NHLF	lung
41	chr4:174091800-174093000	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr4:174091800-174093000	Enhancers	Fetal Intestine Large	intestine
43	chr4:174091800-174093200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr4:174091800-174093600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:174091800-174093600	Enhancers	Fetal Muscle Leg	muscle
46	chr4:174091800-174094600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:174091800-174104000	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr4:174092000-174092600	Enhancers	Primary B cells from cord blood	blood
49	chr4:174092000-174092600	Enhancers	Brain Hippocampus Middle	brain
50	chr4:174092000-174092600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links