Variant report

Variant	rs257377
Chromosome Location	chr7:106801088-106801089
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:106791219..106793947-chr7:106800933..106803916,2	K562	blood:
2	chr7:106799421..106803787-chr7:106805405..106809960,5	MCF-7	breast:
3	chr7:106417789..106419895-chr7:106798550..106801273,2	K562	blood:
4	chr7:106797478..106801451-chr7:106801787..106803813,4	K562	blood:

Variant related genes	Relation type
ENSG00000105856	Chromatin interaction
ENSG00000228742	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1002935	0.84[CEU][hapmap];0.89[AMR][1000 genomes]
rs1018946	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes]
rs1018947	0.84[CEU][hapmap];0.89[AMR][1000 genomes]
rs10248105	1.00[JPT][hapmap]
rs10253172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10261881	0.81[ASN][1000 genomes]
rs10272371	0.88[CHD][hapmap]
rs10487271	0.84[CEU][hapmap]
rs10953529	0.83[AMR][1000 genomes]
rs10953530	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes]
rs10953531	0.84[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes]
rs11509187	0.81[ASN][1000 genomes]
rs11767623	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12055946	0.81[ASN][1000 genomes]
rs12532447	0.89[CEU][hapmap]
rs12532849	0.84[CEU][hapmap]
rs12532953	0.89[AMR][1000 genomes]
rs12533767	0.89[AMR][1000 genomes]
rs12535258	0.84[CEU][hapmap]
rs12536574	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12537374	0.80[AMR][1000 genomes]
rs12537730	0.89[AMR][1000 genomes]
rs12540475	0.80[AMR][1000 genomes]
rs12705405	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17153823	0.88[CHD][hapmap]
rs17153861	0.81[ASN][1000 genomes]
rs17340577	1.00[ASW][hapmap]
rs17341680	0.81[ASN][1000 genomes]
rs17349904	0.84[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes]
rs17424561	1.00[ASW][hapmap]
rs17425839	1.00[ASW][hapmap];0.88[CHD][hapmap]
rs17427123	0.89[AMR][1000 genomes]
rs17427158	0.89[AMR][1000 genomes]
rs17427849	0.89[AMR][1000 genomes]
rs17428071	0.84[CEU][hapmap];0.80[AMR][1000 genomes]
rs17428126	0.80[AMR][1000 genomes]
rs1981696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023892	0.89[AMR][1000 genomes]
rs2107318	0.89[AMR][1000 genomes]
rs2107319	0.84[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs2191917	0.81[ASN][1000 genomes]
rs2249043	0.84[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs2250121	0.88[CHD][hapmap]
rs257371	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257372	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257373	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257375	0.93[CEU][hapmap];0.89[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257379	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257381	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257382	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257385	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257386	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28610544	0.81[ASN][1000 genomes]
rs2894459	0.84[CEU][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap]
rs3729876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3729877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752645	0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs3779500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801963	0.83[CEU][hapmap]
rs3801965	0.84[CEU][hapmap];0.89[AMR][1000 genomes]
rs4727671	0.80[AMR][1000 genomes]
rs4730222	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4730223	0.84[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4730224	0.89[AMR][1000 genomes]
rs4730226	0.80[AMR][1000 genomes]
rs61014091	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61673847	0.80[AMR][1000 genomes]
rs6466160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6946036	0.96[GIH][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes]
rs6946931	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947675	0.82[CEU][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6947857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949961	0.84[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes]
rs6951639	0.89[AMR][1000 genomes]
rs6960148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6960708	0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs6967745	0.84[CEU][hapmap];0.89[AMR][1000 genomes]
rs6971393	0.81[ASN][1000 genomes]
rs6971675	0.84[CEU][hapmap];0.89[AMR][1000 genomes]
rs6971774	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];0.87[AMR][1000 genomes]
rs6977868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978486	0.81[ASN][1000 genomes]
rs7777976	0.80[AMR][1000 genomes]
rs7781947	0.84[CEU][hapmap]
rs7786692	0.88[CHD][hapmap]
rs7789678	0.82[AMR][1000 genomes]
rs7793594	0.80[AMR][1000 genomes]
rs7794598	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs7794915	0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs7794965	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes]
rs7798223	0.89[AMR][1000 genomes]
rs7981	0.81[CEU][hapmap];0.89[AMR][1000 genomes]
rs8180787	0.81[ASN][1000 genomes]
rs9641378	0.84[CEU][hapmap];0.87[AMR][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs257377	BCAP29	cis	parietal	SCAN
rs257377	TAS2R30	trans	lymphoblastoid	seeQTL
rs257377	NRCAM	cis	parietal	SCAN
rs257377	GPR22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106760400-106808400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:106763000-106807800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr7:106778400-106807800	Weak transcription	Brain Germinal Matrix	brain
4	chr7:106780000-106807800	Weak transcription	Fetal Heart	heart
5	chr7:106782600-106808000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:106782800-106807800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:106783600-106807600	Weak transcription	Fetal Stomach	stomach
8	chr7:106784200-106802600	Strong transcription	K562	blood
9	chr7:106785400-106808000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:106785800-106807600	Weak transcription	Fetal Kidney	kidney
11	chr7:106787400-106805800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:106788000-106805800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:106788000-106808000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:106788200-106807600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr7:106788400-106808000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:106788600-106805800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr7:106788800-106805800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr7:106788800-106807200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:106788800-106807600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr7:106788800-106807800	Weak transcription	Ovary	ovary
21	chr7:106789400-106808200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr7:106790000-106807200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:106791000-106805600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr7:106791000-106806800	Weak transcription	Fetal Intestine Large	intestine
25	chr7:106791000-106807600	Weak transcription	Brain Anterior Caudate	brain
26	chr7:106791200-106807800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr7:106792200-106808400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr7:106793000-106804000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:106794000-106807200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:106794000-106808200	Weak transcription	Left Ventricle	heart
31	chr7:106795600-106808400	Weak transcription	Gastric	stomach
32	chr7:106797400-106801400	Strong transcription	Adipose Nuclei	Adipose
33	chr7:106797800-106807600	Weak transcription	Fetal Brain Female	brain
34	chr7:106798200-106807400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:106798400-106807000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:106799200-106805800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr7:106799800-106801400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr7:106800000-106807200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr7:106800200-106807800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr7:106800400-106803200	Weak transcription	HUVEC	blood vessel
41	chr7:106800600-106802200	Enhancers	Fetal Brain Male	brain
42	chr7:106800600-106803600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr7:106800800-106801200	Enhancers	Fetal Lung	lung
44	chr7:106800800-106802800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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