Variant report

Variant	rs6673410
Chromosome Location	chr1:225614140-225614141
allele	A/C
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	JUN	chr1:225611820-225617257	K562	blood:	n/a	chr1:225613227-225613237 chr1:225616567-225616575 chr1:225615250-225615261 chr1:225616568-225616575 chr1:225612971-225612983 chr1:225616565-225616577 chr1:225613226-225613238 chr1:225613227-225613237 chr1:225613228-225613236 chr1:225616567-225616575 chr1:225615989-225615998 chr1:225612930-225612939 chr1:225613227-225613237 chr1:225616648-225616657 chr1:225615862-225615871 chr1:225616566-225616576
2	MAX	chr1:225613853-225616765	NB4	blood:	n/a	chr1:225616368-225616378 chr1:225614720-225614727 chr1:225616566-225616575 chr1:225614718-225614728 chr1:225615632-225615642
3	POLR2A	chr1:225613990-225616782	GM12892	blood:	n/a	n/a
4	FOS	chr1:225613669-225614241	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:225611871-225615203	K562	blood:	n/a	n/a
6	MXI1	chr1:225613968-225616747	IMR90	lung:	n/a	n/a
7	TBP	chr1:225614084-225614286	HepG2	liver:	n/a	n/a
8	CHD1	chr1:225614071-225616836	IMR90	lung:	n/a	chr1:225615951-225615961 chr1:225615306-225615313 chr1:225615930-225615940
9	REST	chr1:225614090-225616919	H1-neurons	neurons:	n/a	chr1:225614567-225614585 chr1:225615143-225615163 chr1:225615628-225615641 chr1:225615409-225615422 chr1:225615612-225615625 chr1:225614778-225614791 chr1:225615226-225615240 chr1:225615617-225615627
10	TEAD4	chr1:225614139-225614413	H1-hESC	embryonic stem cell:	n/a	chr1:225614248-225614257
11	MXI1	chr1:225614100-225616612	Hela-S3	cervix:	n/a	n/a
12	CHD2	chr1:225614138-225614850	GM12878	blood:	n/a	n/a
13	TEAD4	chr1:225613826-225615416	K562	blood:	n/a	chr1:225614248-225614257
14	POLR2A	chr1:225613030-225616753	K562	blood:	n/a	n/a
15	MYC	chr1:225613049-225615057	MCF10A-Er-Src	breast:	n/a	chr1:225614720-225614727 chr1:225614718-225614728 chr1:225613403-225613413
16	POLR2A	chr1:225613874-225617283	Hela-S3	cervix:	n/a	n/a
17	MXI1	chr1:225609788-225616921	SK-N-SH	brain:	n/a	n/a
18	UBTF	chr1:225613917-225616755	K562	blood:	n/a	n/a
19	ZNF263	chr1:225614002-225616632	HEK293-T-REx	kidney:	n/a	chr1:225615583-225615592
20	BACH1	chr1:225614061-225614404	K562	blood:	n/a	n/a
21	MAX	chr1:225614103-225616816	A549	lung:	n/a	chr1:225616368-225616378 chr1:225614720-225614727 chr1:225616566-225616575 chr1:225614718-225614728 chr1:225615632-225615642
22	STAT5A	chr1:225614130-225615329	GM12878	blood:	n/a	chr1:225614502-225614510
23	SMC3	chr1:225613955-225615196	Hela-S3	cervix:	n/a	n/a
24	TBL1XR1	chr1:225613532-225615014	K562	blood:	n/a	n/a
25	SPI1	chr1:225614089-225614732	HL-60	blood:	n/a	n/a
26	TEAD4	chr1:225614020-225614533	H1-hESC	embryonic stem cell:	n/a	chr1:225614248-225614257
27	SIN3A	chr1:225614121-225616729	GM12878	blood:	n/a	chr1:225615322-225615333
28	POLR2A	chr1:225613808-225617160	PBDE	blood:	n/a	n/a
29	MYC	chr1:225613726-225617110	K562	blood:	n/a	chr1:225616368-225616378 chr1:225614720-225614727 chr1:225616566-225616575 chr1:225614718-225614728 chr1:225615632-225615642
30	GTF2F1	chr1:225613892-225614894	Hela-S3	cervix:	n/a	n/a
31	MAZ	chr1:225613873-225616829	K562	blood:	n/a	chr1:225616368-225616378 chr1:225614720-225614727 chr1:225616566-225616575 chr1:225615632-225615642
32	CHD1	chr1:225613919-225614989	GM12878	blood:	n/a	n/a
33	MAX	chr1:225613824-225616666	K562	blood:	n/a	chr1:225616368-225616378 chr1:225614720-225614727 chr1:225616566-225616575 chr1:225614718-225614728 chr1:225615632-225615642
34	NR2F2	chr1:225614120-225615527	K562	blood:	n/a	n/a
35	MXI1	chr1:225614047-225616784	GM12878	blood:	n/a	n/a
36	WRNIP1	chr1:225613856-225615230	GM12878	blood:	n/a	n/a
37	MYC	chr1:225613674-225616825	K562	blood:	n/a	chr1:225616368-225616378 chr1:225614720-225614727 chr1:225616566-225616575 chr1:225614718-225614728 chr1:225615632-225615642

No.	Distal block	Cell Line	Cell type
1	chr1:225605937..225609657-chr1:225612868..225616965,5	MCF-7	breast:
2	chr1:225609832..225612207-chr1:225614120..225615659,2	MCF-7	breast:
3	chr1:225604992..225607166-chr1:225612913..225616218,4	MCF-7	breast:
4	chr1:225613325..225614871-chr1:225640956..225643217,2	K562	blood:
5	chr1:225569904..225572339-chr1:225612601..225615493,2	K562	blood:

Variant related genes	Relation type
LBR	TF binding region
ENSG00000143815	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1537877	1.00[CEU][hapmap]
rs16844879	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16844881	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16844898	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16844899	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6684200	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6692416	1.00[ASW][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7555352	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer 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	20 gene(s)	inside rSNPs	diseases
2	nsv1004851	chr1:225614140-225684184	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225609600-225615200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr1:225609800-225614200	Enhancers	Small Intestine	intestine
3	chr1:225611600-225614200	Enhancers	Primary B cells from peripheral blood	blood
4	chr1:225612000-225614200	Flanking Active TSS	Fetal Brain Female	brain
5	chr1:225612000-225614200	Transcr. at gene 5' and 3'	K562	blood
6	chr1:225612000-225614600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:225612000-225614600	Flanking Active TSS	Brain Germinal Matrix	brain
8	chr1:225612000-225615000	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr1:225612000-225615400	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr1:225612200-225614200	Flanking Active TSS	Colon Smooth Muscle	Colon
11	chr1:225612200-225614200	Enhancers	Gastric	stomach
12	chr1:225612200-225614400	Flanking Active TSS	HMEC	breast
13	chr1:225612200-225614600	Flanking Active TSS	Osteobl	bone
14	chr1:225612200-225614800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr1:225612400-225614200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:225612400-225614200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:225612400-225614200	Enhancers	Brain Substantia Nigra	brain
18	chr1:225612400-225614200	Enhancers	Psoas Muscle	Psoas
19	chr1:225612400-225614200	Flanking Active TSS	GM12878-XiMat	blood
20	chr1:225612400-225614400	Flanking Active TSS	NHEK	skin
21	chr1:225612400-225614600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:225612400-225614600	Enhancers	Spleen	Spleen
23	chr1:225612400-225614800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr1:225612400-225614800	Flanking Active TSS	NH-A	brain
25	chr1:225612400-225615000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr1:225612400-225615200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:225612600-225614200	Flanking Active TSS	HepG2	liver
28	chr1:225612600-225614200	Flanking Active TSS	NHLF	lung
29	chr1:225612600-225614400	Weak transcription	Aorta	Aorta
30	chr1:225612600-225614600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr1:225612600-225615200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr1:225612600-225615200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:225612800-225614200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:225612800-225614400	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr1:225612800-225614400	Flanking Active TSS	Hela-S3	cervix
36	chr1:225612800-225614600	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr1:225612800-225614600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr1:225612800-225614600	Flanking Active TSS	Fetal Thymus	thymus
39	chr1:225613000-225614200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:225613000-225614400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr1:225613000-225614400	Enhancers	Stomach Mucosa	stomach
42	chr1:225613000-225614600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr1:225613000-225614800	Flanking Active TSS	HUVEC	blood vessel
44	chr1:225613200-225614200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr1:225613200-225614400	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr1:225613200-225614600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr1:225613200-225614600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:225613200-225615000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr1:225613200-225615000	Flanking Active TSS	Liver	Liver
50	chr1:225613400-225614200	Weak transcription	Fetal Muscle Trunk	muscle

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