Variant report

Variant	rs6923993
Chromosome Location	chr6:36427276-36427277
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36422087..36425016-chr6:36426919..36429459,2	K562	blood:
2	chr6:36427110..36428848-chr6:36563217..36564833,2	K562	blood:
3	chr6:36410350..36413326-chr6:36427199..36430771,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112078	Chromatin interaction
ENSG00000179165	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1003250	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10440841	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1076929	0.82[CHD][hapmap]
rs10947609	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12209346	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12214285	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215889	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233080	0.84[AMR][1000 genomes]
rs1570368	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1742757	0.81[ASN][1000 genomes]
rs1744654	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2187810	0.80[CHD][hapmap]
rs3752478	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3798471	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4140593	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711450	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4711452	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711453	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs515129	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs515186	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs517890	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs522179	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs544267	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs546272	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs546353	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs547026	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs547966	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs566742	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57389119	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs584196	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584418	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59440875	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs595954	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs597153	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs600192	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs605684	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs609067	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs614028	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs619011	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs621796	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs628213	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs628314	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs629297	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs629560	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs629721	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs632943	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457918	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs648125	0.84[CEU][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes]
rs659726	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs664370	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs668499	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs6906885	0.82[CHD][hapmap]
rs6919571	0.83[CHD][hapmap]
rs6941918	0.81[ASN][1000 genomes]
rs73411054	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7744363	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];0.99[ASN][1000 genomes]
rs853873	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs853881	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853882	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860513	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs863815	0.83[ASN][1000 genomes]
rs9296180	0.83[CHD][hapmap]
rs9296184	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9357214	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470274	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9470278	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9470285	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9470309	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6923993	PPIL1	cis	brain	seeQTL
rs6923993	PNPLA1	cis	cerebellum	SCAN
rs6923993	ETV7	cis	Whole Blood	GTEx
rs6923993	C6orf1	cis	parietal	SCAN
rs6923993	PXT1	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36411600-36439800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:36411600-36476400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:36411800-36439400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:36412200-36449200	Weak transcription	Esophagus	oesophagus
5	chr6:36412400-36437800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:36412400-36438400	Weak transcription	Lung	lung
7	chr6:36412600-36429600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:36412600-36430600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr6:36412600-36430800	Weak transcription	Small Intestine	intestine
10	chr6:36412600-36438600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:36412600-36439200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:36412600-36449000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:36412800-36430800	Weak transcription	Brain Substantia Nigra	brain
14	chr6:36412800-36430800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:36412800-36443400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:36412800-36447000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:36412800-36448600	Weak transcription	HMEC	breast
18	chr6:36413400-36427400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr6:36413400-36429600	Weak transcription	Brain Hippocampus Middle	brain
20	chr6:36413400-36431200	Weak transcription	NHEK	skin
21	chr6:36413400-36431400	Weak transcription	A549	lung
22	chr6:36413400-36437800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr6:36413400-36439200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr6:36413600-36428400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr6:36413600-36429400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr6:36413600-36430800	Weak transcription	NHDF-Ad	bronchial
27	chr6:36413600-36437800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr6:36413800-36427400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:36413800-36429200	Weak transcription	HUVEC	blood vessel
30	chr6:36413800-36429400	Weak transcription	Fetal Heart	heart
31	chr6:36413800-36436800	Weak transcription	Fetal Lung	lung
32	chr6:36415000-36429000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr6:36415800-36428000	Weak transcription	Right Atrium	heart
34	chr6:36415800-36428400	Weak transcription	Aorta	Aorta
35	chr6:36416400-36429800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:36417000-36429600	Weak transcription	Primary B cells from cord blood	blood
37	chr6:36417000-36436400	Weak transcription	HSMM	muscle
38	chr6:36417000-36438400	Weak transcription	Fetal Brain Female	brain
39	chr6:36417200-36430600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:36417200-36438800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:36417200-36439000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr6:36417200-36439200	Weak transcription	Brain Anterior Caudate	brain
43	chr6:36417600-36429400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr6:36417600-36431200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:36417600-36431200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:36417600-36434200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:36417600-36439200	Weak transcription	Spleen	Spleen
48	chr6:36418400-36438400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr6:36419000-36428200	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr6:36419000-36431200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links