Variant report

Variant	rs377931
Chromosome Location	chr19:44438923-44438924
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	chr19:44438871-44439765	MCF10A-Er-Src	breast:	n/a	n/a
2	GABPA	chr19:44438817-44440161	A549	lung:	n/a	chr19:44439497-44439506
3	GATA3	chr19:44438899-44440131	A549	lung:	n/a	chr19:44439290-44439300
4	CTCF	chr19:44438800-44438950	NHDF-neo	bronchial:	n/a	n/a
5	CTCF	chr19:44438880-44439030	GM06990	blood:	n/a	n/a
6	SREBP1	chr19:44438244-44440460	GM12878	blood:	n/a	n/a
7	ZNF263	chr19:44438242-44439825	HEK293-T-REx	kidney:	n/a	chr19:44438663-44438684
8	SIX5	chr19:44438825-44440079	A549	lung:	n/a	chr19:44439458-44439467 chr19:44439456-44439465 chr19:44439454-44439468
9	ETS1	chr19:44438724-44440014	A549	lung:	n/a	chr19:44439422-44439431 chr19:44439510-44439520 chr19:44439707-44439720 chr19:44439497-44439508 chr19:44439509-44439518 chr19:44439415-44439431 chr19:44439455-44439468 chr19:44439422-44439433 chr19:44439509-44439520 chr19:44439520-44439533 chr19:44439423-44439433 chr19:44439454-44439467 chr19:44439483-44439490
10	SIN3AK20	chr19:44438896-44439973	MCF-7	breast:	n/a	n/a
11	CTCF	chr19:44438840-44438990	NHDF-neo	bronchial:	n/a	n/a
12	GABPA	chr19:44438880-44440042	SK-N-SH	brain:	n/a	chr19:44439497-44439506
13	CTCF	chr19:44438906-44439180	IMR90	lung:	n/a	n/a
14	POLR2A	chr19:44438920-44439938	PFSK-1	brain:	n/a	n/a
15	CUX1	chr19:44438758-44439829	K562	blood:	n/a	n/a
16	HCFC1	chr19:44438175-44440337	Hela-S3	cervix:	n/a	n/a
17	CHD1	chr19:44438824-44439884	GM12878	blood:	n/a	n/a
18	TCF12	chr19:44438832-44440084	A549	lung:	n/a	n/a
19	GABPA	chr19:44438610-44440292	MCF-7	breast:	n/a	chr19:44439497-44439506
20	RCOR1	chr19:44438609-44439760	K562	blood:	n/a	n/a
21	MAX	chr19:44438892-44439968	A549	lung:	n/a	n/a
22	CTCF	chr19:44438780-44438930	GM12872	blood:	n/a	n/a
23	MXI1	chr19:44438475-44440059	IMR90	lung:	n/a	n/a
24	MAX	chr19:44438878-44440056	A549	lung:	n/a	n/a
25	RAD21	chr19:44438618-44439247	Hela-S3	cervix:	n/a	n/a
26	SMC3	chr19:44438731-44439697	Hela-S3	cervix:	n/a	chr19:44439499-44439509
27	BRCA1	chr19:44438880-44439683	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr19:44438758-44439554	K562	blood:	n/a	chr19:44439500-44439510 chr19:44439499-44439512 chr19:44439265-44439278
29	CTCF	chr19:44438920-44439070	HCM	heart:	n/a	n/a
30	UBTF	chr19:44438529-44439593	K562	blood:	n/a	n/a
31	REST	chr19:44438850-44440009	H1-neurons	neurons:	n/a	n/a
32	CTCF	chr19:44438920-44439070	HA-sp	spinal cord:	n/a	n/a
33	ELK1	chr19:44438913-44439904	GM12878	blood:	n/a	n/a
34	GABPA	chr19:44438860-44439962	A549	lung:	n/a	chr19:44439497-44439506

No.	Distal block	Cell Line	Cell type
1	chr19:44405165..44406844-chr19:44438913..44440753,2	K562	blood:
2	chr19:44330249..44332710-chr19:44437495..44440338,2	MCF-7	breast:
3	chr19:44330466..44332260-chr19:44438054..44440025,2	K562	blood:

Variant related genes	Relation type
ZNF45	TF binding region
ENSG00000267191	Chromatin interaction
ENSG00000176222	Chromatin interaction
ENSG00000267058	Chromatin interaction
ENSG00000167637	Chromatin interaction
ENSG00000159871	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10402944	0.82[EUR][1000 genomes]
rs2299936	0.84[EUR][1000 genomes]
rs2429734	0.85[EUR][1000 genomes]
rs364278	0.92[CEU][hapmap]
rs366431	0.86[EUR][1000 genomes]
rs376655	0.81[EUR][1000 genomes]
rs381220	0.89[EUR][1000 genomes]
rs381872	0.88[CEU][hapmap];0.88[TSI][hapmap]
rs385202	0.89[EUR][1000 genomes]
rs385578	0.87[EUR][1000 genomes]
rs386249	0.89[EUR][1000 genomes]
rs388547	0.90[EUR][1000 genomes]
rs390134	0.84[EUR][1000 genomes]
rs391961	0.89[EUR][1000 genomes]
rs394132	0.90[EUR][1000 genomes]
rs394380	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs395419	0.87[EUR][1000 genomes]
rs396188	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs397276	0.81[CEU][hapmap]
rs400591	0.96[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs401770	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs413061	0.88[CEU][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs415468	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs415867	0.90[EUR][1000 genomes]
rs418336	0.96[CEU][hapmap]
rs424041	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs427401	0.81[EUR][1000 genomes]
rs429611	0.81[EUR][1000 genomes]
rs437700	0.87[EUR][1000 genomes]
rs439417	0.96[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs441386	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs441742	0.90[EUR][1000 genomes]
rs444816	0.96[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs454376	0.83[GIH][hapmap]

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	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv579854	chr19:44411543-44490024	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers 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	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs377931	CYTH2	cis	parietal	SCAN
rs377931	FOXA3	cis	cerebellum	SCAN
rs377931	KLC3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44438000-44439000	Flanking Active TSS	Primary T cells from cord blood	blood
2	chr19:44438000-44439000	Flanking Active TSS	HUVEC	blood vessel
3	chr19:44438000-44439200	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr19:44438000-44439200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr19:44438000-44439800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:44438000-44440000	Active TSS	GM12878-XiMat	blood
7	chr19:44438000-44440000	Active TSS	NHLF	lung
8	chr19:44438200-44439000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr19:44438200-44439000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr19:44438200-44439000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:44438200-44439000	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr19:44438200-44439000	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr19:44438200-44439200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr19:44438200-44439800	Active TSS	Hela-S3	cervix
15	chr19:44438200-44440000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:44438200-44440200	Active TSS	H1 Cell Line	embryonic stem cell
17	chr19:44438200-44440200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:44438200-44440200	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr19:44438200-44440200	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr19:44438200-44440200	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr19:44438200-44440200	Active TSS	Psoas Muscle	Psoas
22	chr19:44438200-44440600	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr19:44438400-44439000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:44438400-44439000	Enhancers	Spleen	Spleen
25	chr19:44438400-44439200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr19:44438400-44439800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr19:44438400-44439800	Active TSS	Fetal Kidney	kidney
28	chr19:44438400-44439800	Active TSS	Lung	lung
29	chr19:44438400-44440000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:44438400-44440000	Active TSS	Right Atrium	heart
31	chr19:44438400-44440000	Active TSS	Right Ventricle	heart
32	chr19:44438400-44440200	Active TSS	Fetal Intestine Small	intestine
33	chr19:44438600-44439000	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr19:44438600-44439200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:44438600-44439600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:44438600-44439800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:44438600-44439800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:44438600-44439800	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr19:44438600-44440000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr19:44438600-44440000	Active TSS	H9 Cell Line	embryonic stem cell
41	chr19:44438600-44440000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:44438600-44440000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr19:44438600-44440000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:44438600-44440000	Active TSS	Aorta	Aorta
45	chr19:44438600-44440000	Active TSS	Fetal Brain Female	brain
46	chr19:44438600-44440000	Active TSS	NHDF-Ad	bronchial
47	chr19:44438600-44440200	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr19:44438600-44440600	Active TSS	Thymus	Thymus
49	chr19:44438800-44439200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:44438800-44439200	Flanking Active TSS	Placenta Amnion	Placenta Amnion

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