Variant report

Variant	rs34637472
Chromosome Location	chr19:44126279-44126280
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:44122432-44126679	HepG2	liver:	n/a	n/a
2	ZC3H11A	chr19:44126197-44126311	K562	blood:	n/a	n/a
3	POLR2A	chr19:44126180-44126286	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:44125760-44126491	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:44097500..44104541-chr19:44116930..44130620,31	K562	blood:
2	chr19:44124320..44127049-chr19:44284895..44287840,2	K562	blood:
3	chr19:44122279..44128380-chr19:44171168..44174381,7	K562	blood:
4	chr19:44097777..44104240-chr19:44121602..44130880,30	K562	blood:
5	chr19:44118551..44131201-chr19:44135615..44147023,20	K562	blood:
6	chr19:44126223..44128182-chr19:44135324..44137117,2	MCF-7	breast:
7	chr19:44121917..44126953-chr19:44140515..44144634,11	MCF-7	breast:
8	chr19:44126234..44128942-chr19:44160943..44162925,2	K562	blood:

No data

Variant related genes	Relation type
ZNF428	TF binding region
ENSG00000226763	Chromatin interaction
ENSG00000104783	Chromatin interaction
ENSG00000011422	Chromatin interaction
ENSG00000105767	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000167378	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10402946	0.92[ASW][hapmap];0.97[LWK][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs17655646	0.86[CEU][hapmap]
rs2240633	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2270075	0.93[AFR][1000 genomes]
rs304719	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs304720	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs304722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs304723	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs304726	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34521657	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35346236	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs365063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3803910	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs427115	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4803646	0.82[CEU][hapmap]
rs4803647	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7245651	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8101956	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][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	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv833839	chr19:44099813-44272299	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs34637472	ELSPBP1	cis	cerebellum	SCAN
rs34637472	IZUMO2	cis	parietal	SCAN
rs34637472	PRRG2	cis	cerebellum	SCAN
rs34637472	STRN4	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44124400-44126800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:44124600-44126800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:44124600-44127200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:44124600-44127600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:44124600-44127600	Weak transcription	Placenta	Placenta
6	chr19:44124600-44127800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:44124600-44128200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:44124600-44129000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr19:44124600-44129200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr19:44124600-44130200	Weak transcription	Esophagus	oesophagus
11	chr19:44124600-44143400	Weak transcription	Right Atrium	heart
12	chr19:44124800-44127200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr19:44124800-44127200	Weak transcription	Brain Anterior Caudate	brain
14	chr19:44124800-44128800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr19:44124800-44128800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr19:44124800-44128800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:44124800-44128800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:44124800-44129000	Weak transcription	Primary B cells from cord blood	blood
19	chr19:44124800-44129000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:44124800-44129600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:44124800-44129800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr19:44124800-44131200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr19:44124800-44138400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr19:44124800-44138800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr19:44124800-44139000	Weak transcription	Colon Smooth Muscle	Colon
26	chr19:44125000-44126600	Weak transcription	Brain Germinal Matrix	brain
27	chr19:44125000-44127200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr19:44125000-44127200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr19:44125000-44127200	Weak transcription	Fetal Intestine Small	intestine
30	chr19:44125000-44127400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr19:44125000-44127400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr19:44125000-44127400	Weak transcription	Brain Hippocampus Middle	brain
33	chr19:44125000-44127400	Weak transcription	Brain Substantia Nigra	brain
34	chr19:44125000-44127800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr19:44125000-44128000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:44125000-44128200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr19:44125000-44128600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr19:44125000-44128800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr19:44125000-44128800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:44125000-44128800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:44125000-44128800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:44125000-44128800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr19:44125000-44129000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr19:44125000-44129000	Weak transcription	Small Intestine	intestine
45	chr19:44125000-44129200	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr19:44125000-44129200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:44125000-44130400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr19:44125000-44130400	Weak transcription	Gastric	stomach
49	chr19:44125000-44130400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr19:44125000-44130800	Weak transcription	Stomach Smooth Muscle	stomach

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