Variant report

Variant	rs7426999
Chromosome Location	chr3:52001071-52001072
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	POLR2A	chr3:52001030-52002404	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr3:52001000-52001150	SAEC	small airway:	n/a	n/a
3	SMARCB1	chr3:52000924-52002227	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr3:52001000-52001150	GM12872	blood:	n/a	n/a
5	CTCF	chr3:52001020-52001170	HRE	kidney:	n/a	n/a
6	ZBTB7A	chr3:52000806-52002473	ECC-1	luminal epithelium:	n/a	chr3:52002005-52002016
7	EBF1	chr3:52001013-52001300	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:52000604-52004386	HepG2	liver:	n/a	n/a
9	MAX	chr3:52000959-52003042	HepG2	liver:	n/a	chr3:52002253-52002263
10	CTCF	chr3:52001020-52001170	GM12872	blood:	n/a	n/a
11	POLR2A	chr3:52000993-52002724	H1-neurons	neurons:	n/a	n/a
12	POLR2A	chr3:52001037-52001502	K562	blood:	n/a	n/a
13	POLR2A	chr3:52000905-52002797	H1-neurons	neurons:	n/a	n/a
14	POLR2A	chr3:52001054-52001419	HepG2	liver:	n/a	n/a
15	MXI1	chr3:52000907-52002412	IMR90	lung:	n/a	n/a
16	POLR2A	chr3:52001050-52002378	HCT-116	colon:	n/a	n/a
17	SIN3A	chr3:52001041-52002724	H1-hESC	embryonic stem cell:	n/a	chr3:52001042-52001056 chr3:52002033-52002046
18	CTCF	chr3:52001060-52001210	AG04449	skin:	n/a	n/a
19	CTCF	chr3:52001060-52001210	GM12871	blood:	n/a	n/a
20	CTCF	chr3:52001040-52001190	GM12874	blood:	n/a	n/a
21	SMC3	chr3:52000928-52001453	Hela-S3	cervix:	n/a	n/a
22	MAZ	chr3:52000663-52002637	IMR90	lung:	n/a	chr3:52002253-52002263
23	CTCF	chr3:52001040-52001190	BJ	skin:	n/a	n/a
24	CHD1	chr3:52000913-52001418	IMR90	lung:	n/a	n/a
25	MAZ	chr3:52000990-52002392	GM12878	blood:	n/a	chr3:52002253-52002263
26	MXI1	chr3:52000959-52001287	GM12878	blood:	n/a	n/a
27	REST	chr3:52000680-52002949	H1-neurons	neurons:	n/a	chr3:52000755-52000768 chr3:52002487-52002500 chr3:52001970-52001983 chr3:52001041-52001061 chr3:52001961-52001979 chr3:52002033-52002046 chr3:52002331-52002344 chr3:52001963-52001976 chr3:52001141-52001154 chr3:52002454-52002467
28	TCF7L2	chr3:52000989-52002162	HCT-116	colon:	n/a	n/a
29	ZBTB7A	chr3:52000994-52002818	ECC-1	luminal epithelium:	n/a	chr3:52002005-52002016
30	MAX	chr3:52001009-52001643	ECC-1	luminal epithelium:	n/a	n/a
31	EP300	chr3:52000908-52001505	ECC-1	luminal epithelium:	n/a	chr3:52000976-52000989
32	ELF1	chr3:52000829-52002584	GM12878	blood:	n/a	chr3:52001964-52001976 chr3:52001478-52001490
33	MXI1	chr3:51999719-52003632	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr3:52000980-52003171	Hela-S3	cervix:	n/a	n/a
35	CTCF	chr3:52000980-52001130	HBMEC	blood vessel:	n/a	n/a
36	CTCF	chr3:52001040-52001190	GM12873	blood:	n/a	n/a
37	POLR2A	chr3:52000308-52002203	K562	blood:	n/a	n/a
38	CHD2	chr3:52000996-52002698	Hela-S3	cervix:	n/a	chr3:52002329-52002339

No.	Distal block	Cell Line	Cell type
1	chr3:51974673..51977845-chr3:51999030..52003727,6	K562	blood:
2	chr3:51996322..51998656-chr3:51999527..52001457,4	MCF-7	breast:
3	chr3:51974263..51976425-chr3:51999030..52003412,4	K562	blood:
4	chr3:51997248..52000056-chr3:52000079..52001783,2	MCF-7	breast:
5	chr3:51976807..51978359-chr3:51999918..52002472,2	K562	blood:
6	chr3:51972287..51978873-chr3:51998179..52003667,9	MCF-7	breast:
7	chr3:51966649..51968588-chr3:51999482..52001370,2	K562	blood:

Variant related genes	Relation type
PCBP4	TF binding region
ABHD14A	TF binding region
ENSG00000090097	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000114767	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12632925	1.00[CHD][hapmap]
rs178918	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323869	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323870	0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323872	0.96[LWK][hapmap];1.00[MKK][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323878	1.00[AMR][1000 genomes]
rs323880	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323883	1.00[MEX][hapmap]
rs323889	0.88[LWK][hapmap];0.96[MKK][hapmap];1.00[AMR][1000 genomes]
rs323891	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323896	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323900	0.88[LWK][hapmap];0.96[MKK][hapmap];1.00[AMR][1000 genomes]
rs34821455	1.00[CHD][hapmap]
rs368210	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs422304	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687604	1.00[CHD][hapmap]
rs56746340	1.00[AMR][1000 genomes]
rs57384151	1.00[AMR][1000 genomes]
rs6446141	1.00[AMR][1000 genomes]
rs72961930	1.00[AMR][1000 genomes]
rs72961999	1.00[AMR][1000 genomes]
rs72964016	1.00[AMR][1000 genomes]
rs7636204	0.84[LWK][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs9683234	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv876781	chr3:51985664-52009612	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv876782	chr3:51985664-52022779	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	nsv876783	chr3:51987224-52009612	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv876784	chr3:51987224-52013242	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv876785	chr3:51994881-52022779	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
15	esv3403794	chr3:52000337-52003085	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51996600-52001200	Enhancers	Fetal Brain Male	brain
2	chr3:51996600-52001200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr3:51997800-52001200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:51998600-52001200	Flanking Active TSS	Brain Angular Gyrus	brain
5	chr3:51999000-52001200	Flanking Active TSS	Fetal Brain Female	brain
6	chr3:51999200-52001200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:51999200-52001200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:51999600-52001200	Flanking Active TSS	HepG2	liver
9	chr3:51999800-52001200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:51999800-52001200	Flanking Active TSS	HMEC	breast
11	chr3:51999800-52001400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:51999800-52001400	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr3:52000000-52001200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:52000000-52001200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:52000000-52001200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr3:52000000-52001200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:52000000-52001200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
18	chr3:52000000-52001200	Flanking Active TSS	HSMM	muscle
19	chr3:52000200-52001200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:52000200-52001200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:52000200-52001200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
22	chr3:52000200-52001200	Flanking Active TSS	Fetal Muscle Leg	muscle
23	chr3:52000200-52001200	Flanking Active TSS	Right Ventricle	heart
24	chr3:52000200-52001400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:52000200-52002000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:52000200-52002200	Active TSS	HSMMtube	muscle
27	chr3:52000400-52001200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:52000400-52001200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:52000400-52001200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr3:52000400-52001200	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr3:52000400-52001200	Flanking Active TSS	Fetal Heart	heart
32	chr3:52000400-52001200	Flanking Active TSS	Fetal Stomach	stomach
33	chr3:52000400-52001200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
34	chr3:52000400-52001200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr3:52000400-52001200	Flanking Active TSS	HUVEC	blood vessel
36	chr3:52000400-52001400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:52000400-52001400	Flanking Active TSS	Dnd41	blood
38	chr3:52000400-52002000	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr3:52000400-52002600	Active TSS	Fetal Kidney	kidney
40	chr3:52000400-52002600	Active TSS	Rectal Smooth Muscle	rectum
41	chr3:52000600-52001200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:52000600-52001200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:52000600-52001200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
44	chr3:52000600-52001200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
45	chr3:52000600-52001200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr3:52000600-52001200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr3:52000600-52001200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:52000600-52001200	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr3:52000600-52001200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
50	chr3:52000600-52001200	Flanking Active TSS	Fetal Intestine Small	intestine

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