Variant report

Variant	rs6465885
Chromosome Location	chr7:102577433-102577434
allele	C/T
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	chr7:102577390-102577892	K562	blood:	n/a	n/a
2	EP300	chr7:102573385-102577692	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:102574165..102576650-chr7:102576864..102579530,2	K562	blood:
2	chr7:102574165..102576596-chr7:102576864..102579639,2	K562	blood:

Variant related genes	Relation type
FBXL13	TF binding region
ENSG00000161040	Chromatin interaction
ENSG00000128606	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10257543	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10267275	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap]
rs10273725	0.85[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10435335	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10487279	0.81[ASW][hapmap]
rs10487283	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10499952	0.91[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1057066	0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10808120	0.81[GIH][hapmap]
rs1100044	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11543736	0.91[EUR][1000 genomes]
rs11970869	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11972019	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11972644	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11973870	0.92[EUR][1000 genomes]
rs11978670	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11978768	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[EUR][1000 genomes]
rs11978799	0.85[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11980643	0.88[EUR][1000 genomes]
rs11981980	0.91[MEX][hapmap];0.90[TSI][hapmap]
rs11983456	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.92[EUR][1000 genomes]
rs11983521	0.90[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[EUR][1000 genomes]
rs12056296	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12532495	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12533386	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12540384	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12666317	0.82[GIH][hapmap]
rs12666764	0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[EUR][1000 genomes]
rs12667218	0.92[EUR][1000 genomes]
rs12668434	0.91[MEX][hapmap];0.90[TSI][hapmap]
rs12669668	0.90[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap]
rs12671803	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13242493	0.93[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17136090	0.91[MEX][hapmap];0.90[TSI][hapmap]
rs17136137	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2009503	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2159022	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2190673	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2228686	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2411056	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2411059	0.99[EUR][1000 genomes]
rs35479298	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3779029	0.92[EUR][1000 genomes]
rs41501847	0.85[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4296965	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4357217	0.81[ASW][hapmap]
rs56894117	0.92[EUR][1000 genomes]
rs56921864	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57350619	0.92[EUR][1000 genomes]
rs57368671	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57545514	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57616389	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57776797	0.92[EUR][1000 genomes]
rs58191643	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58680618	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58814323	0.80[EUR][1000 genomes]
rs59278165	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60524601	0.92[EUR][1000 genomes]
rs60599650	0.92[EUR][1000 genomes]
rs61679881	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6465877	0.91[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6465878	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6465879	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6465882	0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6942855	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6945369	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs6946773	0.90[ASW][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap]
rs6947403	0.93[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6949150	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6951288	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs6953980	0.85[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6956781	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6957434	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6957771	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6967389	0.90[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[EUR][1000 genomes]
rs6968713	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6973081	0.90[ASW][hapmap];0.84[LWK][hapmap];0.90[MKK][hapmap];0.81[AFR][1000 genomes]
rs6975451	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6976005	0.92[EUR][1000 genomes]
rs6977145	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73406284	0.95[EUR][1000 genomes]
rs73406302	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73408204	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73408241	0.80[AMR][1000 genomes]
rs73408250	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7779121	0.81[ASW][hapmap]
rs7779145	0.85[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7779618	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7780405	0.85[CEU][hapmap];0.90[GIH][hapmap]
rs7780981	0.91[MEX][hapmap];0.90[TSI][hapmap]
rs7785272	0.82[GIH][hapmap]
rs7796335	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7804322	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs847646	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs847647	0.93[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs847652	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs847656	0.93[CEU][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs847658	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs865865	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs955992	0.85[CEU][hapmap]
rs9690210	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv464667	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv608060	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6465885	LRWD1	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102517200-102578200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:102571400-102579600	Genic enhancers	HSMM	muscle
3	chr7:102571600-102581800	Weak transcription	Fetal Intestine Small	intestine
4	chr7:102571800-102579400	Weak transcription	Left Ventricle	heart
5	chr7:102573000-102577600	Genic enhancers	Fetal Stomach	stomach
6	chr7:102573200-102578200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:102573400-102578600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr7:102573400-102579400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:102573400-102579800	Genic enhancers	Fetal Lung	lung
10	chr7:102573800-102591400	Weak transcription	Pancreas	Pancrea
11	chr7:102574000-102592200	Weak transcription	Fetal Intestine Large	intestine
12	chr7:102574200-102579600	Weak transcription	Colon Smooth Muscle	Colon
13	chr7:102574400-102577600	Enhancers	Fetal Kidney	kidney
14	chr7:102574400-102578800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr7:102574600-102577600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:102574600-102594400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr7:102574800-102577600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr7:102574800-102578400	Weak transcription	Fetal Brain Female	brain
19	chr7:102574800-102579800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr7:102575000-102584400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr7:102575000-102586000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr7:102575000-102586800	Weak transcription	NHLF	lung
23	chr7:102575400-102577600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:102575400-102577600	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr7:102575400-102578600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr7:102575400-102578800	Weak transcription	Small Intestine	intestine
27	chr7:102575400-102587000	Strong transcription	NH-A	brain
28	chr7:102575600-102577600	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr7:102575600-102578400	Weak transcription	HUVEC	blood vessel
30	chr7:102575600-102578800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:102575600-102578800	Weak transcription	Liver	Liver
32	chr7:102575600-102579000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr7:102575600-102579400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr7:102575600-102581600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr7:102575600-102583000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:102575600-102585200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr7:102575600-102586800	Weak transcription	Osteobl	bone
38	chr7:102576000-102579800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr7:102576800-102578200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr7:102576800-102578400	Weak transcription	Adipose Nuclei	Adipose
41	chr7:102576800-102579400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr7:102576800-102582000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:102576800-102582400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr7:102576800-102582400	Weak transcription	NHDF-Ad	bronchial
45	chr7:102576800-102584000	Weak transcription	Fetal Muscle Leg	muscle
46	chr7:102576800-102584200	Weak transcription	Aorta	Aorta
47	chr7:102577000-102577800	Strong transcription	Fetal Brain Male	brain
48	chr7:102577000-102578200	Weak transcription	Stomach Mucosa	stomach
49	chr7:102577000-102578600	Weak transcription	HSMMtube	muscle
50	chr7:102577000-102579400	Weak transcription	H9 Cell Line	embryonic stem cell

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