Variant report

Variant	rs4917014
Chromosome Location	chr7:50305863-50305864
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50301953..50306241-chr7:50308308..50311979,4	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11185602	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11185603	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17552904	0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs17634369	0.95[JPT][hapmap]
rs1870027	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4385425	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4598207	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55935382	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62445350	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62447171	0.82[ASN][1000 genomes]
rs876036	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs876037	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs876038	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs876039	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[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	nsv464444	chr7:49671882-50454736	Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv606897	chr7:49671883-50454736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv498090	chr7:49708644-50427714	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1020869	chr7:49712860-50457544	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1024102	chr7:50195864-50418159	Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Systemic lupus erythematosus	19838193	GWAS catalog
HDL cholesterol	24097068	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4917014	IKZF1	cis	parietal	SCAN
rs4917014	LOC100129427	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50298000-50306200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr7:50299000-50306000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr7:50300000-50306000	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr7:50300200-50306000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr7:50300800-50306400	Enhancers	Primary hematopoietic stem cells	blood
6	chr7:50301000-50306400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr7:50301200-50306200	Enhancers	K562	blood
8	chr7:50301800-50306200	Enhancers	Primary B cells from cord blood	blood
9	chr7:50301800-50306200	Enhancers	Primary B cells from peripheral blood	blood
10	chr7:50301800-50310000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr7:50303400-50306200	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr7:50304800-50306000	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr7:50305000-50306200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:50305000-50306200	Enhancers	GM12878-XiMat	blood
15	chr7:50305000-50306600	Enhancers	Duodenum Mucosa	Duodenum
16	chr7:50305000-50307800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr7:50305200-50310400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr7:50305400-50306000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:50305400-50307800	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr7:50305600-50306000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr7:50305600-50306200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr7:50305600-50306400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr7:50305600-50306800	Enhancers	H1 Cell Line	embryonic stem cell
24	chr7:50305600-50307000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr7:50305600-50307200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr7:50305600-50307600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr7:50305600-50307600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr7:50305600-50307600	Flanking Active TSS	Fetal Thymus	thymus
29	chr7:50305600-50308200	Enhancers	Spleen	Spleen
30	chr7:50305600-50308600	Flanking Active TSS	Dnd41	blood
31	chr7:50305800-50306600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
32	chr7:50305800-50306600	Enhancers	H9 Cell Line	embryonic stem cell
33	chr7:50305800-50306600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr7:50305800-50306800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr7:50305800-50307000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr7:50305800-50307400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr7:50305800-50307400	Enhancers	Colonic Mucosa	Colon
38	chr7:50305800-50307400	Flanking Active TSS	Thymus	Thymus
39	chr7:50305800-50307600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links