Variant report

Variant	rs17640544
Chromosome Location	chr19:38917095-38917096
allele	C/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	TEAD4	chr19:38916757-38917131	K562	blood:	n/a	n/a
2	EBF1	chr19:38916450-38917140	GM12878	blood:	n/a	chr19:38916687-38916696 chr19:38916687-38916697 chr19:38916814-38916825 chr19:38916816-38916825 chr19:38916687-38916696 chr19:38916814-38916827 chr19:38916501-38916510
3	CTCF	chr19:38916859-38917218	K562	blood:	n/a	n/a
4	CHD2	chr19:38916763-38917150	K562	blood:	n/a	n/a
5	ATF2	chr19:38916774-38917148	GM12878	blood:	n/a	n/a
6	MAZ	chr19:38916599-38917164	K562	blood:	n/a	chr19:38916751-38916761
7	MTA3	chr19:38916520-38917151	GM12878	blood:	n/a	n/a
8	GATA2	chr19:38916921-38917108	SH-SY5Y	brain:	n/a	n/a
9	CBX3	chr19:38916715-38917110	K562	blood:	n/a	n/a
10	CHD2	chr19:38916643-38917104	GM12878	blood:	n/a	n/a
11	TBL1XR1	chr19:38916878-38917118	GM12878	blood:	n/a	n/a
12	RUNX3	chr19:38916713-38917140	GM12878	blood:	n/a	n/a
13	MAZ	chr19:38916768-38917154	GM12878	blood:	n/a	n/a
14	RCOR1	chr19:38916723-38917151	K562	blood:	n/a	n/a
15	JUND	chr19:38916708-38917137	K562	blood:	n/a	n/a
16	SPI1	chr19:38916535-38917127	GM12878	blood:	n/a	chr19:38916891-38916904 chr19:38916852-38916865 chr19:38916855-38916864 chr19:38916852-38916865 chr19:38916853-38916866
17	NFIC	chr19:38916713-38917204	GM12878	blood:	n/a	n/a
18	TBL1XR1	chr19:38916476-38917459	K562	blood:	n/a	n/a
19	IRF1	chr19:38916798-38917402	K562	blood:	n/a	chr19:38917274-38917287 chr19:38917274-38917285 chr19:38917179-38917192 chr19:38917275-38917285 chr19:38917273-38917287 chr19:38916845-38916865 chr19:38917179-38917193 chr19:38917020-38917033 chr19:38917274-38917287 chr19:38916851-38916865 chr19:38917275-38917289
20	ELF1	chr19:38916638-38917208	GM12878	blood:	n/a	n/a
21	IKZF1	chr19:38916924-38917173	GM12878	blood:	n/a	n/a
22	GABPA	chr19:38916647-38917104	K562	blood:	n/a	n/a
23	EP300	chr19:38916767-38917232	K562	blood:	n/a	n/a
24	ZMIZ1	chr19:38916711-38917148	K562	blood:	n/a	n/a
25	STAT5A	chr19:38916912-38917141	GM12878	blood:	n/a	n/a
26	YY1	chr19:38916762-38917109	GM12892	blood:	n/a	chr19:38916924-38916935
27	FOXM1	chr19:38916759-38917184	GM12878	blood:	n/a	n/a
28	RUNX3	chr19:38916711-38917192	GM12878	blood:	n/a	n/a
29	CTCF	chr19:38916980-38917130	GM12872	blood:	n/a	n/a
30	CTCF	chr19:38916869-38917154	GM12878	blood:	n/a	n/a
31	EP300	chr19:38917092-38917292	GM12878	blood:	n/a	chr19:38917276-38917290

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38891977..38893968-chr19:38915428..38917384,2	K562	blood:

Variant related genes	Relation type
RASGRP4	TF binding region
ENSG00000130244	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11878707	1.00[TSI][hapmap]
rs11880126	1.00[MEX][hapmap]
rs11883126	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12971920	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12972609	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12972895	1.00[EUR][1000 genomes]
rs12973210	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12974363	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12974979	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12975212	0.96[EUR][1000 genomes]
rs12982894	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12986359	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34026587	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34158728	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34377632	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34411591	0.92[AFR][1000 genomes]
rs34456672	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34898849	0.92[AFR][1000 genomes]
rs35136248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35710536	1.00[TSI][hapmap]
rs71356804	1.00[EUR][1000 genomes]
rs71356805	1.00[EUR][1000 genomes]
rs9916978	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1055309	chr19:38896244-38945851	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv1065803	chr19:38903099-38945851	Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv1066138	chr19:38904072-38949729	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv833824	chr19:38914618-39084758	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17640544	SH2D1A	trans	lymphoblastoid	seeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38915800-38917200	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr19:38916000-38917200	Enhancers	Primary T cells from cord blood	blood
3	chr19:38916000-38917200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:38916000-38917400	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr19:38916000-38917400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:38916000-38917600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr19:38916000-38917600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:38916000-38918000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr19:38916200-38917200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr19:38916200-38917200	Enhancers	Dnd41	blood
11	chr19:38916200-38917400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr19:38916200-38917600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr19:38916200-38918400	Enhancers	Primary B cells from peripheral blood	blood
14	chr19:38916200-38918400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:38916200-38918600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr19:38916200-38918800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr19:38916400-38917200	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr19:38916400-38917200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr19:38916400-38920600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr19:38916600-38918000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:38916600-38918400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:38916800-38917200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr19:38916800-38917600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr19:38916800-38917600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:38916800-38917600	Enhancers	Fetal Thymus	thymus
26	chr19:38916800-38918200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:38916800-38918200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr19:38916800-38920200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr19:38916800-38924000	Weak transcription	Right Atrium	heart
30	chr19:38917000-38917200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr19:38917000-38917200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr19:38917000-38917400	Flanking Active TSS	K562	blood
33	chr19:38917000-38917600	Flanking Active TSS	GM12878-XiMat	blood
34	chr19:38917000-38917600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr19:38917000-38920600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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