Variant report

Variant	rs3801964
Chromosome Location	chr7:106836242-106836243
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	chr7:106829648-106836708	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:106828513..106831475-chr7:106834925..106836469,2	K562	blood:
2	chr7:106829518..106831320-chr7:106836010..106838979,2	K562	blood:

Variant related genes	Relation type
HBP1	TF binding region
ENSG00000272072	TF binding region
ENSG00000105856	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12112877	0.81[ASN][1000 genomes]
rs12670688	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12672451	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13230144	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17153981	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2107317	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2237658	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237659	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237660	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237661	0.95[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2237662	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2237665	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2283038	0.90[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301801	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2395868	0.89[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2395869	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34021916	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3801966	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4730220	0.87[ASN][1000 genomes]
rs62482493	0.81[ASN][1000 genomes]
rs62483619	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62483623	0.84[ASN][1000 genomes]
rs62483627	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62483629	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62483633	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62483634	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62483640	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62483641	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7785892	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7803151	0.87[EUR][1000 genomes];0.88[ASN][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	nsv831087	chr7:106673465-106872460	Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS 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	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3801964	BCAP29	Cis_1M	lymphoblastoid	RTeQTL
rs3801964	COG5	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106810600-106836800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:106815200-106849400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr7:106816000-106843600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:106817400-106851400	Strong transcription	Primary B cells from peripheral blood	blood
5	chr7:106819600-106851800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr7:106819800-106846600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr7:106819800-106851600	Strong transcription	Dnd41	blood
8	chr7:106820000-106851200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr7:106820000-106851600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr7:106820200-106837000	Weak transcription	Psoas Muscle	Psoas
11	chr7:106820200-106848400	Strong transcription	Placenta	Placenta
12	chr7:106820200-106851200	Strong transcription	Primary B cells from cord blood	blood
13	chr7:106820200-106851800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:106820200-106851800	Strong transcription	Fetal Thymus	thymus
15	chr7:106820400-106845200	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr7:106820400-106848200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:106821000-106840000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr7:106821000-106848400	Strong transcription	Liver	Liver
19	chr7:106821000-106854600	Strong transcription	Primary T cells from cord blood	blood
20	chr7:106821200-106841600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:106821200-106845800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr7:106821200-106846600	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr7:106821200-106851800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr7:106821200-106851800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr7:106821200-106851800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr7:106821400-106837200	Weak transcription	Stomach Mucosa	stomach
27	chr7:106821400-106851800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr7:106821600-106851600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr7:106821600-106851800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr7:106821800-106839600	Weak transcription	Small Intestine	intestine
31	chr7:106821800-106847800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr7:106821800-106851400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr7:106822000-106847400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:106822400-106842000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr7:106823000-106851200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr7:106823800-106849600	Weak transcription	HMEC	breast
37	chr7:106825200-106842200	Strong transcription	Brain Hippocampus Middle	brain
38	chr7:106828600-106837000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr7:106828600-106843800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr7:106828600-106849600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:106828600-106851800	Strong transcription	Fetal Intestine Large	intestine
42	chr7:106828800-106836400	Weak transcription	NHEK	skin
43	chr7:106828800-106842000	Strong transcription	Adipose Nuclei	Adipose
44	chr7:106828800-106849800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr7:106828800-106851200	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr7:106830000-106836400	Weak transcription	NH-A	brain
47	chr7:106830400-106846600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr7:106830800-106837600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr7:106831400-106844400	Weak transcription	Right Ventricle	heart
50	chr7:106831400-106847800	Weak transcription	Fetal Brain Male	brain

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