Variant report

Variant	rs431978
Chromosome Location	chr6:149793000-149793001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149785728..149788361-chr6:149790642..149793612,2	K562	blood:
2	chr6:149792520..149794344-chr6:149794518..149797030,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11155656	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11155657	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs112225	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12190660	0.84[ASN][1000 genomes]
rs1737336	0.87[ASN][1000 genomes]
rs1737337	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1749227	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1768341	0.80[ASN][1000 genomes]
rs1999970	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2095849	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs237004	0.93[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap]
rs367133	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs367161	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs367812	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs370471	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs372994	0.87[ASN][1000 genomes]
rs373596	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs374616	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs376269	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs376757	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs377454	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs377532	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs378991	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs381226	0.92[CEU][hapmap];0.93[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs381793	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs382084	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs382720	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs383092	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs384163	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs384306	0.91[CEU][hapmap];0.93[CHB][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs384913	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs385303	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs388335	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs391875	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs392928	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs392932	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs393713	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs394375	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs394526	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs395037	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs398159	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs403419	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs405486	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs407260	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs408451	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs409196	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs410579	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs411091	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs411308	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs416044	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs419562	0.87[ASN][1000 genomes]
rs419997	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs425278	0.86[CEU][hapmap];0.93[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs431362	0.88[CEU][hapmap];0.94[CHB][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs432582	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs436645	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs437931	0.87[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs439369	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs439495	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs440613	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs450344	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs452586	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs499270	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs543489	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs602010	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs602094	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs677525	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs786749	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs786750	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs786751	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs786757	0.83[ASN][1000 genomes]
rs814181	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9485396	0.81[EUR][1000 genomes];0.85[ASN][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	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv470866	chr6:149744632-149806552	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv5533	chr6:149748047-149793072	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv464076	chr6:149755695-149798835	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv604846	chr6:149755695-149798835	ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv1832313	chr6:149789511-149840750	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs431978	RAET1E	cis	cerebellum	SCAN
rs431978	LRP11	cis	cerebellum	SCAN
rs431978	LRP11	cis	parietal	SCAN
rs431978	SUMO4	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149776800-149802000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:149780800-149793400	Weak transcription	Primary T cells from cord blood	blood
3	chr6:149781400-149793800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:149782200-149802000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:149783200-149802400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:149783800-149793400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr6:149785800-149793400	Weak transcription	Hela-S3	cervix
8	chr6:149785800-149794600	Weak transcription	Gastric	stomach
9	chr6:149785800-149794800	Weak transcription	Right Atrium	heart
10	chr6:149786000-149794200	Weak transcription	Colonic Mucosa	Colon
11	chr6:149786200-149793400	Weak transcription	Stomach Mucosa	stomach
12	chr6:149788200-149795200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:149788400-149794600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:149789000-149794400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:149789200-149793800	Weak transcription	HepG2	liver
16	chr6:149789400-149806000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:149789600-149798400	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr6:149789800-149793400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr6:149789800-149795200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:149790000-149793000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr6:149790000-149793200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:149790000-149796000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:149790200-149793800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:149790200-149794200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:149790200-149802000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:149790400-149793200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr6:149790400-149794000	Weak transcription	Fetal Thymus	thymus
28	chr6:149790400-149794400	Genic enhancers	Primary B cells from peripheral blood	blood
29	chr6:149790400-149795000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr6:149790400-149802200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:149790600-149795600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr6:149790800-149795600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr6:149791000-149794600	Weak transcription	Lung	lung
34	chr6:149791000-149799000	Genic enhancers	Primary B cells from cord blood	blood
35	chr6:149791200-149793400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr6:149792000-149796400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr6:149792000-149800200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:149792400-149793600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:149792400-149793800	Weak transcription	Fetal Intestine Small	intestine
40	chr6:149792400-149795200	Flanking Active TSS	GM12878-XiMat	blood
41	chr6:149792600-149795400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:149792600-149803000	Weak transcription	Fetal Brain Female	brain
43	chr6:149792800-149793200	Weak transcription	Spleen	Spleen
44	chr6:149792800-149793600	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr6:149792800-149796200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
46	chr6:149792800-149797000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:149793000-149793200	Enhancers	Thymus	Thymus
48	chr6:149793000-149794200	Enhancers	Duodenum Mucosa	Duodenum

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