Variant report

Variant	rs1978443
Chromosome Location	chr19:39091033-39091034
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	POLR2A	chr19:39090609-39091242	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:39090496-39091423	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:39090425-39091327	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:39090847-39091423	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:39090649-39091383	GM12891	blood:	n/a	n/a
6	TCF7L2	chr19:39091018-39091366	PANC-1	pancreas:	n/a	chr19:39091225-39091241 chr19:39091226-39091240 chr19:39091229-39091238 chr19:39091225-39091241
7	POLR2A	chr19:39090413-39091243	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39086632..39088965-chr19:39089842..39091395,2	K562	blood:
2	chr19:39090721..39094839-chr19:39095384..39098942,6	K562	blood:

Variant related genes	Relation type
MAP4K1	TF binding region
ENSG00000267291	Chromatin interaction
ENSG00000104814	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10404936	0.91[LWK][hapmap];0.81[YRI][hapmap]
rs10445564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12977469	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs13345885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1862371	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs2232992	0.87[CEU][hapmap];0.83[TSI][hapmap]
rs2287732	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2287733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3786834	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4592774	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802618	0.94[LWK][hapmap];0.81[YRI][hapmap]
rs60803495	0.92[ASN][1000 genomes]
rs62120354	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62120358	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6508809	0.81[YRI][hapmap]
rs7251456	0.81[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs750438	0.82[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs888994	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	nsv911665	chr19:38924814-39101879	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1978443	LYPD4	cis	parietal	SCAN
rs1978443	PLAUR	cis	cerebellum	SCAN
rs1978443	AP2S1	cis	cerebellum	SCAN
rs1978443	TMEM145	cis	parietal	SCAN
rs1978443	ZFP36	cis	parietal	SCAN
rs1978443	SELV	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39070600-39100000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:39074800-39101600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr19:39076600-39093200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:39076800-39092800	Strong transcription	Primary B cells from peripheral blood	blood
5	chr19:39077000-39101600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr19:39077200-39103200	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr19:39077800-39093000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:39078200-39092200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:39086400-39096600	Weak transcription	Fetal Thymus	thymus
10	chr19:39086400-39098400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr19:39086800-39096600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:39087200-39107800	Weak transcription	Colonic Mucosa	Colon
13	chr19:39087400-39107400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr19:39087400-39108200	Weak transcription	Gastric	stomach
15	chr19:39087400-39108800	Weak transcription	Right Atrium	heart
16	chr19:39088200-39091800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:39088200-39096200	Weak transcription	Spleen	Spleen
18	chr19:39088400-39096600	Weak transcription	Dnd41	blood
19	chr19:39088400-39098400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr19:39088600-39096200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr19:39088600-39100200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr19:39089200-39094200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr19:39090000-39091400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr19:39090000-39092600	Strong transcription	Primary T cells from cord blood	blood
25	chr19:39090200-39091400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr19:39090400-39091200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr19:39090400-39091200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:39090400-39091200	Strong transcription	Thymus	Thymus
29	chr19:39090400-39091200	Strong transcription	GM12878-XiMat	blood
30	chr19:39090400-39092400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:39090400-39092600	Strong transcription	Primary B cells from cord blood	blood
32	chr19:39090600-39092200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr19:39090800-39091200	Enhancers	K562	blood
34	chr19:39090800-39094600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:39091000-39094400	Weak transcription	Monocytes-CD14+_RO01746	blood

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