Variant report

Variant	rs7699787
Chromosome Location	chr4:152575079-152575080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152568195..152570506-chr4:152573252..152576175,2	K562	blood:

Extended variants
information (count: 131 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10001439	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10009423	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10025109	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10031175	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10857261	0.86[EUR][1000 genomes]
rs11099813	0.83[EUR][1000 genomes]
rs11099818	0.89[EUR][1000 genomes]
rs11099824	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11556167	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs11723643	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11726171	0.83[EUR][1000 genomes]
rs11726222	0.89[EUR][1000 genomes]
rs11726545	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11728541	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11729514	0.89[EUR][1000 genomes]
rs11729871	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11730733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11732441	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11732453	0.80[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11735143	0.89[EUR][1000 genomes]
rs11736961	0.89[EUR][1000 genomes]
rs11934818	0.89[EUR][1000 genomes]
rs11947720	0.87[EUR][1000 genomes]
rs12054502	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12498556	0.89[EUR][1000 genomes]
rs12498878	0.89[EUR][1000 genomes]
rs12502212	0.89[EUR][1000 genomes]
rs12502967	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12504273	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12508678	0.89[EUR][1000 genomes]
rs12511280	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1366908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1366910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs1372979	0.89[EUR][1000 genomes]
rs1443085	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17027716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs17027818	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17275584	0.97[EUR][1000 genomes]
rs17275605	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17275612	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17360294	0.89[CEU][hapmap]
rs17360378	0.89[CEU][hapmap]
rs1992517	0.89[EUR][1000 genomes]
rs2406972	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28417319	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28447105	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28463438	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28483174	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28498882	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28527216	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28545583	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28574706	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28605105	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28608075	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28608757	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28672085	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28706249	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28715753	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3172567	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35588363	0.81[EUR][1000 genomes]
rs36083376	0.89[EUR][1000 genomes]
rs3762906	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs3792689	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs3934474	0.89[EUR][1000 genomes]
rs4371601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4385035	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4622982	0.87[EUR][1000 genomes]
rs56092201	0.89[EUR][1000 genomes]
rs56199243	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56763519	0.86[EUR][1000 genomes]
rs57272881	0.89[EUR][1000 genomes]
rs57348790	0.82[EUR][1000 genomes]
rs57556564	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58443173	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58961701	0.85[EUR][1000 genomes]
rs59731141	0.89[EUR][1000 genomes]
rs59744221	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59811197	0.87[EUR][1000 genomes]
rs59984665	0.89[EUR][1000 genomes]
rs60077220	0.89[EUR][1000 genomes]
rs60122169	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60169090	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60618075	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60707008	0.89[EUR][1000 genomes]
rs61294884	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61302767	0.89[EUR][1000 genomes]
rs61630225	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6535802	0.89[EUR][1000 genomes]
rs6535805	0.90[CEU][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs6812000	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6817373	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6822729	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6822737	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6826318	0.89[EUR][1000 genomes]
rs6832899	0.89[EUR][1000 genomes]
rs6832902	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6833277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6835310	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6838608	0.87[EUR][1000 genomes]
rs6839738	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6841515	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6843267	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6844169	0.89[EUR][1000 genomes]
rs6845067	0.89[EUR][1000 genomes]
rs6846013	0.89[EUR][1000 genomes]
rs6846759	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6853342	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6856392	0.85[EUR][1000 genomes]
rs6858573	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72962929	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73861826	0.86[EUR][1000 genomes]
rs73861827	0.86[EUR][1000 genomes]
rs73862055	0.89[EUR][1000 genomes]
rs73862076	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73862080	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73862085	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73864013	0.86[EUR][1000 genomes]
rs7438281	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7653926	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7655466	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7662214	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[EUR][1000 genomes]
rs7662713	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7664074	0.89[EUR][1000 genomes]
rs7671456	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7677528	0.89[EUR][1000 genomes]
rs7696468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs9683881	0.83[EUR][1000 genomes]
rs9917912	0.89[EUR][1000 genomes]
rs9996600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9999456	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755535	chr4:152549395-152609395	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7699787	LRBA	cis	cerebellum	SCAN
rs7699787	FAM160A1	cis	cerebellum	SCAN
rs7699787	SH3D19	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152545600-152578600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:152561000-152579400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:152562600-152577400	Weak transcription	HMEC	breast
4	chr4:152563800-152625200	Weak transcription	Hela-S3	cervix
5	chr4:152564200-152595200	Weak transcription	Aorta	Aorta
6	chr4:152566000-152577200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:152567400-152608600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr4:152567800-152609000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:152568200-152577800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:152568600-152577200	Weak transcription	Colonic Mucosa	Colon
11	chr4:152570600-152582200	Weak transcription	Spleen	Spleen
12	chr4:152570800-152579200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:152571000-152577200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:152571200-152584200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:152571200-152584200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:152571400-152577400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:152571400-152577400	Weak transcription	Fetal Intestine Large	intestine
18	chr4:152571400-152577400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:152571600-152583600	Weak transcription	Ovary	ovary
20	chr4:152571600-152595000	Weak transcription	HepG2	liver
21	chr4:152571800-152577200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:152571800-152577200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:152571800-152577200	Weak transcription	Fetal Intestine Small	intestine
24	chr4:152571800-152577400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:152571800-152577400	Weak transcription	Esophagus	oesophagus
26	chr4:152571800-152577800	Weak transcription	Liver	Liver
27	chr4:152571800-152578000	Weak transcription	Gastric	stomach
28	chr4:152571800-152578000	Weak transcription	Lung	lung
29	chr4:152571800-152578200	Weak transcription	Fetal Stomach	stomach
30	chr4:152572000-152578000	Weak transcription	NHEK	skin
31	chr4:152572200-152577200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr4:152572400-152578600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:152572600-152575400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:152572600-152576800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:152572800-152577200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr4:152572800-152577200	Weak transcription	Pancreas	Pancrea
37	chr4:152572800-152577400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:152572800-152577400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:152573400-152576200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr4:152573800-152576200	Enhancers	Psoas Muscle	Psoas
41	chr4:152573800-152576400	Enhancers	NHDF-Ad	bronchial
42	chr4:152574200-152577200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr4:152574200-152578600	Weak transcription	Right Ventricle	heart
44	chr4:152574400-152576200	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr4:152574400-152578000	Weak transcription	Left Ventricle	heart
46	chr4:152574400-152582800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr4:152574600-152577200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:152574600-152579600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:152574800-152575200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:152574800-152575600	Enhancers	Fetal Thymus	thymus

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