Variant report

Variant	rs376269
Chromosome Location	chr6:149795154-149795155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149637666..149639444-chr6:149793847..149796038,2	K562	blood:
2	chr6:149795137..149796969-chr6:149800706..149802832,2	K562	blood:
3	chr6:149792520..149794344-chr6:149794518..149797030,2	K562	blood:

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs11155656	0.91[ASN][1000 genomes]
rs11155657	0.92[ASN][1000 genomes]
rs112225	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12190660	0.91[ASN][1000 genomes]
rs1737336	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1737337	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1749227	0.91[ASN][1000 genomes]
rs1768341	0.86[ASN][1000 genomes]
rs1999970	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2095849	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs237004	0.93[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap]
rs237006	0.80[ASN][1000 genomes]
rs237007	0.80[ASN][1000 genomes]
rs237015	0.82[JPT][hapmap]
rs237027	0.83[JPT][hapmap]
rs237032	0.83[JPT][hapmap]
rs237033	0.83[JPT][hapmap]
rs367133	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs367161	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs367812	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs370471	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs372994	0.93[ASN][1000 genomes]
rs373596	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs374616	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs376757	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs377454	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs377532	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs378991	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs381226	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs381793	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs382084	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs382720	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383092	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs384163	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs384306	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384913	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs385303	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs385657	0.80[ASN][1000 genomes]
rs388335	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs391875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392928	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs392932	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs393713	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs394375	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs394526	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs395037	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs398159	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403419	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs405486	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs407260	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs408451	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs409196	1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs410579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs411091	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs411308	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs414956	0.80[ASN][1000 genomes]
rs416044	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs416262	0.80[ASN][1000 genomes]
rs419562	0.93[ASN][1000 genomes]
rs419997	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs421037	0.81[ASN][1000 genomes]
rs425278	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs430192	0.80[ASN][1000 genomes]
rs431362	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs431978	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]
rs432582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436645	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs437931	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs439369	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs439495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs440613	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs450344	0.93[ASN][1000 genomes]
rs452586	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs474726	0.83[JPT][hapmap]
rs480670	0.83[JPT][hapmap]
rs484969	0.83[JPT][hapmap]
rs499270	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs500860	0.83[JPT][hapmap]
rs506573	0.83[JPT][hapmap]
rs506779	0.83[JPT][hapmap]
rs538706	0.83[JPT][hapmap]
rs543489	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs558044	0.83[JPT][hapmap]
rs567816	0.83[JPT][hapmap]
rs569730	0.83[JPT][hapmap]
rs580499	0.83[JPT][hapmap]
rs602010	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs602094	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs611311	0.81[ASN][1000 genomes]
rs677525	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7742990	0.83[JPT][hapmap]
rs7747354	0.81[MEX][hapmap]
rs786749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs786750	0.89[ASN][1000 genomes]
rs786751	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs786757	0.89[ASN][1000 genomes]
rs814181	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9485396	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs376269	SUMO4	cis	cerebellum	SCAN
rs376269	RAET1E	cis	cerebellum	SCAN
rs376269	LRP11	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149776800-149802000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:149782200-149802000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:149783200-149802400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:149788200-149795200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:149789400-149806000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:149789600-149798400	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr6:149789800-149795200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:149790000-149796000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
9	chr6:149790200-149802000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:149790400-149802200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:149790600-149795600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr6:149790800-149795600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr6:149791000-149799000	Genic enhancers	Primary B cells from cord blood	blood
14	chr6:149792000-149796400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:149792000-149800200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:149792400-149795200	Flanking Active TSS	GM12878-XiMat	blood
17	chr6:149792600-149795400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:149792600-149803000	Weak transcription	Fetal Brain Female	brain
19	chr6:149792800-149796200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
20	chr6:149792800-149797000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:149793200-149801800	Weak transcription	Thymus	Thymus
22	chr6:149793400-149795400	Enhancers	Primary T cells from cord blood	blood
23	chr6:149793400-149795400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr6:149793400-149796600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
25	chr6:149793800-149795400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr6:149794000-149795200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:149794000-149796000	Enhancers	Fetal Thymus	thymus
28	chr6:149794200-149795200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr6:149794200-149795200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr6:149794200-149795400	Flanking Active TSS	Hela-S3	cervix
31	chr6:149794200-149795800	Enhancers	Adipose Nuclei	Adipose
32	chr6:149794200-149795800	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr6:149794200-149796000	Active TSS	Rectal Smooth Muscle	rectum
34	chr6:149794200-149796000	Enhancers	Right Ventricle	heart
35	chr6:149794200-149796200	Weak transcription	Small Intestine	intestine
36	chr6:149794200-149796400	Enhancers	Spleen	Spleen
37	chr6:149794400-149795200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr6:149794400-149795200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:149794400-149795200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:149794400-149795400	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr6:149794400-149795400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
42	chr6:149794400-149798000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr6:149794400-149800000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:149794600-149795200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:149794600-149795200	Enhancers	Gastric	stomach
46	chr6:149794600-149795200	Enhancers	Lung	lung
47	chr6:149794600-149795600	Flanking Active TSS	Colonic Mucosa	Colon
48	chr6:149794600-149795600	Enhancers	Fetal Intestine Small	intestine
49	chr6:149794600-149795600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr6:149794600-149796000	Enhancers	Stomach Mucosa	stomach

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