Variant report

Variant	rs3846775
Chromosome Location	chr6:87952491-87952492
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:87951720..87954611-chr6:87956928..87959093,2	K562	blood:
2	chr6:87947826..87949359-chr6:87951504..87953481,2	MCF-7	breast:
3	chr6:87863816..87866381-chr6:87949981..87953455,3	MCF-7	breast:
4	chr6:87864079..87866947-chr6:87950535..87952710,3	MCF-7	breast:
5	chr6:87951859..87954369-chr6:87959843..87962210,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188994	Chromatin interaction
ENSG00000272008	Chromatin interaction

Extended variants
information (count: 178 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:176)

rs_ID	r²[population]
rs1080595	0.86[ASN][1000 genomes]
rs1080596	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1201409	0.82[ASN][1000 genomes]
rs12176253	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12190280	0.82[ASN][1000 genomes]
rs12664578	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs173333	0.83[ASN][1000 genomes]
rs1753154	0.94[ASN][1000 genomes]
rs1813847	0.80[EUR][1000 genomes]
rs1813848	0.80[EUR][1000 genomes]
rs183599	0.82[ASN][1000 genomes]
rs1886751	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1886752	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1925688	0.80[EUR][1000 genomes]
rs1925689	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1925695	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1980790	0.86[ASN][1000 genomes]
rs1980791	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1980792	0.86[ASN][1000 genomes]
rs2025630	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2031518	0.86[ASN][1000 genomes]
rs2147917	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2147918	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2147919	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2147920	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2147921	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2182181	0.88[ASN][1000 genomes]
rs2240459	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2240460	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs242267	0.82[ASN][1000 genomes]
rs242270	0.82[ASN][1000 genomes]
rs242278	0.83[ASN][1000 genomes]
rs242279	0.83[ASN][1000 genomes]
rs242280	0.82[ASN][1000 genomes]
rs242281	0.82[ASN][1000 genomes]
rs242283	0.92[ASN][1000 genomes]
rs2474349	0.94[ASN][1000 genomes]
rs2985039	0.86[ASN][1000 genomes]
rs35788380	0.85[EUR][1000 genomes]
rs369674	0.84[ASN][1000 genomes]
rs3734187	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs373646	0.82[ASN][1000 genomes]
rs376633	0.84[ASN][1000 genomes]
rs3812130	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3812132	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs381782	0.86[ASN][1000 genomes]
rs3846773	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846774	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846776	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857483	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3857484	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3857485	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857488	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3903920	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3904088	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4099964	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4110984	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4110985	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs445434	0.86[ASN][1000 genomes]
rs446851	0.83[ASN][1000 genomes]
rs447077	0.83[ASN][1000 genomes]
rs448580	0.86[ASN][1000 genomes]
rs4489129	0.80[EUR][1000 genomes]
rs451089	0.86[ASN][1000 genomes]
rs451465	0.84[ASN][1000 genomes]
rs451829	0.86[ASN][1000 genomes]
rs4533962	0.81[EUR][1000 genomes]
rs4540237	0.81[EUR][1000 genomes]
rs4574603	0.87[EUR][1000 genomes]
rs4591818	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4605853	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4706289	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4707346	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4707347	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4707348	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4707351	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4707352	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4707356	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4707357	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4707358	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs586771	0.82[ASN][1000 genomes]
rs62439492	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6454589	0.88[EUR][1000 genomes]
rs6454590	0.82[ASN][1000 genomes]
rs6454591	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6454592	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6454593	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6454594	0.90[ASN][1000 genomes]
rs6454595	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6454596	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6454597	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6454598	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6454599	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6454600	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6899394	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6904310	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6907805	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6909021	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6909200	0.86[ASN][1000 genomes]
rs6910991	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913721	0.88[ASN][1000 genomes]
rs6913932	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6914193	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6916994	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6917432	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6921007	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6921504	0.82[ASN][1000 genomes]
rs6921619	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6925648	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6926563	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6926831	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6926838	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6927748	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6932678	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933046	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6934603	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6937874	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6940544	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7453986	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7739034	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7739726	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7742478	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7742710	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7748191	0.86[ASN][1000 genomes]
rs7748879	0.87[ASN][1000 genomes]
rs7752485	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7752882	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7753030	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7755244	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755883	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7757199	0.80[EUR][1000 genomes]
rs7757827	0.84[ASN][1000 genomes]
rs7758618	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763365	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7766324	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7767449	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7768575	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7774080	0.88[EUR][1000 genomes]
rs7774603	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7776407	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs910563	0.82[ASN][1000 genomes]
rs9294367	0.80[EUR][1000 genomes]
rs9294372	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9294374	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9344690	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9344691	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9344693	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9344695	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344696	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9344697	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9351114	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9351117	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9351124	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9353455	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9353462	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9353463	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9353464	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9353465	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9353466	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9353468	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9353473	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9359734	0.87[EUR][1000 genomes]
rs9359740	0.81[ASN][1000 genomes]
rs9359743	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9362401	0.80[ASN][1000 genomes]
rs9362408	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9362411	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9362413	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9362415	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9362417	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9444479	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450634	0.88[ASN][1000 genomes]
rs9450647	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450650	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450652	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs994170	0.80[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	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3846775	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs3846775	C6orf163	Cis_1M	lymphoblastoid	RTeQTL
rs3846775	C6orf162	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87884000-87964400	Weak transcription	NHEK	skin
2	chr6:87888200-87964200	Weak transcription	HSMMtube	muscle
3	chr6:87891000-87956000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:87906200-87956200	Weak transcription	A549	lung
5	chr6:87906400-87964400	Weak transcription	NHLF	lung
6	chr6:87910600-87956000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr6:87922200-87956200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:87923200-87953600	Weak transcription	Stomach Mucosa	stomach
9	chr6:87923200-87956000	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:87923400-87955600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:87923400-87956200	Weak transcription	Gastric	stomach
12	chr6:87923400-87956200	Weak transcription	Small Intestine	intestine
13	chr6:87923400-87969000	Weak transcription	Psoas Muscle	Psoas
14	chr6:87924000-87956200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:87924400-87966000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:87924600-87956200	Weak transcription	Right Ventricle	heart
17	chr6:87928000-87956200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr6:87930600-87954000	Weak transcription	HMEC	breast
19	chr6:87933200-87956200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:87933600-87956200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:87933600-87956200	Weak transcription	Lung	lung
22	chr6:87933600-87956400	Weak transcription	Esophagus	oesophagus
23	chr6:87933800-87956200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:87933800-87956200	Weak transcription	Colonic Mucosa	Colon
25	chr6:87934000-87956200	Weak transcription	Left Ventricle	heart
26	chr6:87934000-87956400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:87934200-87954600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:87934400-87953400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr6:87934400-87955600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr6:87934600-87953600	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:87934600-87964200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr6:87934600-87964400	Weak transcription	Brain Angular Gyrus	brain
33	chr6:87934600-87967000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr6:87934800-87953600	Weak transcription	Brain Substantia Nigra	brain
35	chr6:87934800-87954800	Weak transcription	NH-A	brain
36	chr6:87934800-87956000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr6:87934800-87956200	Weak transcription	Brain Anterior Caudate	brain
38	chr6:87934800-87956400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:87934800-87958600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr6:87934800-87964200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr6:87935000-87956200	Weak transcription	HUVEC	blood vessel
42	chr6:87935200-87963400	Weak transcription	Hela-S3	cervix
43	chr6:87935200-87963600	Weak transcription	NHDF-Ad	bronchial
44	chr6:87935800-87956800	Weak transcription	Osteobl	bone
45	chr6:87936400-87961600	Weak transcription	Right Atrium	heart
46	chr6:87936800-87964200	Weak transcription	Fetal Brain Male	brain
47	chr6:87938000-87956000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:87938200-87953200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:87938400-87955000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:87938600-87955400	Weak transcription	Adipose Nuclei	Adipose

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