Variant report

Variant	rs6919423
Chromosome Location	chr6:109558471-109558472
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109556893..109560362-chr6:109702019..109704753,3	K562	blood:
2	chr6:109555640..109560553-chr6:109624000..109628580,4	K562	blood:
3	chr6:109554938..109560362-chr6:109702019..109707132,8	K562	blood:
4	chr6:109556933..109558499-chr6:109629340..109630936,2	K562	blood:

Variant related genes	Relation type
ENSG00000135535	Chromatin interaction
ENSG00000203799	Chromatin interaction
ENSG00000260273	Chromatin interaction
ENSG00000201023	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1008084	0.84[CEU][hapmap]
rs11153161	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11153168	0.87[CEU][hapmap]
rs11964178	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11966072	0.83[CEU][hapmap]
rs12176068	0.82[EUR][1000 genomes]
rs1260593	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs1260595	0.92[CEU][hapmap]
rs1260596	0.92[CEU][hapmap]
rs1269172	0.83[EUR][1000 genomes]
rs1271693	0.84[ASN][1000 genomes]
rs1271697	0.83[EUR][1000 genomes]
rs13196219	0.83[CEU][hapmap]
rs13196590	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13200047	0.88[CEU][hapmap]
rs13211313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13211944	0.90[ASN][1000 genomes]
rs1341271	0.84[CEU][hapmap]
rs1341272	0.92[CEU][hapmap]
rs171272	0.83[EUR][1000 genomes]
rs1741921	0.82[EUR][1000 genomes]
rs1741923	0.92[ASN][1000 genomes]
rs1741930	0.92[CEU][hapmap]
rs1761608	0.92[CEU][hapmap]
rs1766814	0.82[EUR][1000 genomes]
rs2483913	0.82[EUR][1000 genomes]
rs34774766	0.92[ASN][1000 genomes]
rs351716	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs351717	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs351718	0.94[ASN][1000 genomes]
rs351719	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs351720	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs351721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs351722	0.94[ASN][1000 genomes]
rs351723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs351724	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs351725	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs351726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs351727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs351728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs351730	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs351731	0.90[ASN][1000 genomes]
rs351732	0.89[ASN][1000 genomes]
rs351735	0.90[ASN][1000 genomes]
rs351736	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs351737	0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs351742	0.92[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs351743	0.81[EUR][1000 genomes]
rs351744	0.96[ASN][1000 genomes]
rs351746	0.92[ASN][1000 genomes]
rs351747	0.92[ASN][1000 genomes]
rs351749	0.83[EUR][1000 genomes]
rs351750	0.92[ASN][1000 genomes]
rs351751	0.93[ASN][1000 genomes]
rs351752	0.83[EUR][1000 genomes]
rs353052	0.90[ASN][1000 genomes]
rs368467	0.92[CEU][hapmap]
rs371960	0.92[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs377436	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs378447	0.83[EUR][1000 genomes]
rs381565	0.83[EUR][1000 genomes]
rs386696	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs388526	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs392820	0.81[EUR][1000 genomes]
rs396000	0.92[CEU][hapmap]
rs396635	0.92[ASN][1000 genomes]
rs398944	0.82[EUR][1000 genomes]
rs399561	0.92[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs408944	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs410449	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs412754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs418093	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs419106	0.92[CEU][hapmap]
rs419998	0.81[EUR][1000 genomes]
rs421790	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs422113	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs427960	0.92[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs429534	0.92[ASN][1000 genomes]
rs435611	0.83[EUR][1000 genomes]
rs436880	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs437779	0.81[EUR][1000 genomes]
rs440849	0.82[EUR][1000 genomes]
rs442405	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs445796	0.82[EUR][1000 genomes]
rs446974	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs448496	0.93[ASN][1000 genomes]
rs449736	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs449850	0.92[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs455839	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs458185	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs458740	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs459956	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs461487	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs463503	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs463916	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs566164	0.83[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs59673	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6568571	0.87[CEU][hapmap]
rs6925339	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7748918	0.84[CEU][hapmap]
rs830552	0.93[ASN][1000 genomes]
rs830553	0.80[EUR][1000 genomes]
rs830554	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs830556	0.93[ASN][1000 genomes]
rs9320278	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9374080	0.84[CEU][hapmap]
rs9374081	0.83[CEU][hapmap]
rs9384701	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9386774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9386775	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9386796	0.84[CEU][hapmap]
rs9398188	0.83[EUR][1000 genomes]
rs9400272	0.84[CEU][hapmap]
rs9400273	0.83[CEU][hapmap]
rs9480910	0.82[EUR][1000 genomes]
rs9487048	0.83[CEU][hapmap]
rs9791268	0.81[YRI][hapmap]

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	nsv527657	chr6:109533385-109579675	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6919423	RAB40AL	trans	parietal	SCAN
rs6919423	ZBTB24	cis	parietal	SCAN
rs6919423	CD164	cis	parietal	SCAN
rs6919423	GSTM2P1	cis	parietal	SCAN
rs6919423	ATG5	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109552200-109559000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr6:109553800-109558600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:109556800-109558600	Enhancers	Adipose Nuclei	Adipose
4	chr6:109556800-109562800	Enhancers	Primary hematopoietic stem cells	blood
5	chr6:109556800-109564200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:109557000-109560600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:109557200-109559200	Enhancers	Primary B cells from peripheral blood	blood
8	chr6:109557200-109562000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:109557200-109565000	Enhancers	NHDF-Ad	bronchial
10	chr6:109557400-109558600	Enhancers	Duodenum Mucosa	Duodenum
11	chr6:109557400-109559200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:109557400-109559400	Flanking Active TSS	K562	blood
13	chr6:109557400-109562000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr6:109557400-109562200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:109557600-109559400	Enhancers	Lung	lung
16	chr6:109557600-109559600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr6:109557600-109562000	Enhancers	Stomach Mucosa	stomach
18	chr6:109557600-109565200	Enhancers	Hela-S3	cervix
19	chr6:109557800-109558800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr6:109557800-109559000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:109557800-109559200	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr6:109557800-109559400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr6:109557800-109559400	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr6:109557800-109559400	Enhancers	Spleen	Spleen
25	chr6:109558000-109558800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr6:109558000-109558800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr6:109558000-109558800	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr6:109558000-109559000	Enhancers	Primary T cells fromperipheralblood	blood
29	chr6:109558000-109559400	Enhancers	Primary T cells from cord blood	blood
30	chr6:109558000-109560000	Weak transcription	Right Atrium	heart
31	chr6:109558000-109560200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:109558000-109562000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr6:109558200-109558600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:109558200-109558600	Enhancers	HMEC	breast
35	chr6:109558200-109558800	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr6:109558200-109558800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr6:109558200-109558800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:109558200-109559000	Enhancers	HSMM	muscle
39	chr6:109558200-109559400	Enhancers	HUVEC	blood vessel
40	chr6:109558200-109559800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr6:109558200-109560000	Weak transcription	Brain Substantia Nigra	brain
42	chr6:109558200-109560400	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:109558200-109560400	Weak transcription	Fetal Intestine Large	intestine
44	chr6:109558200-109565000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr6:109558200-109565200	Enhancers	Osteobl	bone
46	chr6:109558200-109572200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr6:109558400-109558600	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr6:109558400-109558600	Enhancers	HSMMtube	muscle
49	chr6:109558400-109558800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
50	chr6:109558400-109558800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links