Variant report

Variant	rs205262
Chromosome Location	chr6:34563164-34563165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34557484..34560082-chr6:34560932..34564487,4	K562	blood:
2	chr6:34535096..34537769-chr6:34560989..34563955,2	K562	blood:
3	chr6:34553065..34556672-chr6:34559907..34563488,3	K562	blood:
4	chr6:34553634..34556369-chr6:34563010..34564695,2	MCF-7	breast:
5	chr6:34558125..34560108-chr6:34562262..34564582,2	MCF-7	breast:
6	chr6:34559418..34564619-chr6:34574111..34579705,5	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11961041	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11968972	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1201872	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs1201873	0.82[AFR][1000 genomes]
rs1201874	0.85[AFR][1000 genomes]
rs13209544	0.81[CHB][hapmap];0.90[ASN][1000 genomes]
rs16892384	0.84[ASN][1000 genomes]
rs16892386	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs188190	1.00[ASW][hapmap];0.85[LWK][hapmap];0.80[MEX][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs205258	0.89[AFR][1000 genomes]
rs205259	0.89[AFR][1000 genomes]
rs205260	0.85[YRI][hapmap]
rs205261	0.93[ASN][1000 genomes]
rs205263	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs205264	0.93[ASN][1000 genomes]
rs205265	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs205266	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs205267	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs205284	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs205286	0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs2235568	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs2235569	0.93[ASW][hapmap];0.81[LWK][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs2262245	0.87[AFR][1000 genomes]
rs2744943	0.93[ASW][hapmap];0.82[LWK][hapmap]
rs2744949	0.87[ASW][hapmap];0.82[LWK][hapmap]
rs2744961	0.81[ASW][hapmap];0.82[LWK][hapmap]
rs2744974	1.00[ASW][hapmap];0.85[LWK][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs2814945	0.93[ASW][hapmap];0.82[LWK][hapmap]
rs2814947	0.80[ASW][hapmap]
rs2814971	0.93[ASW][hapmap]
rs2814972	0.88[YRI][hapmap];0.88[AFR][1000 genomes]
rs2814974	0.81[AFR][1000 genomes]
rs2814976	0.88[YRI][hapmap];0.86[AFR][1000 genomes]
rs2814979	0.87[AFR][1000 genomes]
rs2814981	1.00[ASW][hapmap];0.85[LWK][hapmap];0.80[MEX][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs2814984	1.00[ASW][hapmap];0.85[LWK][hapmap];0.80[MEX][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs2814992	0.93[ASW][hapmap];0.82[LWK][hapmap]
rs34374374	0.93[ASN][1000 genomes]
rs35286877	0.84[ASN][1000 genomes]
rs35987776	0.84[ASN][1000 genomes]
rs36032186	0.94[ASN][1000 genomes]
rs412392	0.85[YRI][hapmap];0.85[AFR][1000 genomes]
rs451263	0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs451603	0.92[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6457784	0.91[ASN][1000 genomes]
rs6900426	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6908462	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs6909637	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6937428	0.84[ASN][1000 genomes]
rs6941453	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs7738377	0.88[ASN][1000 genomes]
rs7743724	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs7764921	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7765969	0.83[ASN][1000 genomes]
rs9380455	0.93[ASW][hapmap];0.82[LWK][hapmap]
rs9461992	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9461993	0.83[ASN][1000 genomes]
rs9461994	0.84[ASN][1000 genomes]
rs9461997	0.84[ASN][1000 genomes]
rs9469812	0.92[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9469813	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs9469814	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs9469820	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9469822	0.88[ASN][1000 genomes]
rs9469832	0.90[ASN][1000 genomes]
rs9469836	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs9469837	0.84[ASN][1000 genomes]
rs9469838	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9469840	0.84[ASN][1000 genomes]
rs9469842	0.84[ASN][1000 genomes]
rs9469859	0.93[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv2758046	chr6:34382492-34714677	Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2759418	chr6:34382492-34714677	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv885785	chr6:34404636-34874002	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv1033583	chr6:34471572-34828372	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv885792	chr6:34507311-34607958	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv885793	chr6:34520267-34886436	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv823667	chr6:34533015-34592524	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv818410	chr6:34538544-34579431	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv830640	chr6:34542489-34714677	Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv885794	chr6:34561585-34673149	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs205262	UHRF1BP1	cis	Adipose Subcutaneous	GTEx
rs205262	C6orf107	cis	uninvolved skin	skin_eQTL
rs205262	UHRF1BP1	cis	Esophagus Muscularis	GTEx
rs205262	SNRPC	cis	parietal	SCAN
rs205262	UHRF1BP1	cis	Artery Tibial	GTEx
rs205262	UHRF1BP1	cis	Whole Blood	GTEx
rs205262	UHRF1BP1	cis	Muscle Skeletal	GTEx
rs205262	UHRF1BP1	cis	Artery Aorta	GTEx
rs205262	C6orf89	cis	parietal	SCAN
rs205262	UHRF1BP1	cis	Nerve Tibial	GTEx
rs205262	SNRPC	cis	cerebellum	SCAN
rs205262	CPNE5	cis	cerebellum	SCAN
rs205262	UHRF1BP1	cis	lung	GTEx
rs205262	UGT2B17	trans	lymphoblastoid	seeQTL
rs205262	C6orf107	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34535600-34563200	Weak transcription	A549	lung
2	chr6:34547200-34566800	Weak transcription	Aorta	Aorta
3	chr6:34549000-34564200	Strong transcription	Fetal Intestine Small	intestine
4	chr6:34549400-34564400	Weak transcription	Brain Substantia Nigra	brain
5	chr6:34549800-34564200	Strong transcription	Fetal Stomach	stomach
6	chr6:34553400-34570000	Weak transcription	NH-A	brain
7	chr6:34553600-34566400	Weak transcription	Brain Germinal Matrix	brain
8	chr6:34554000-34573600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:34554600-34577200	Weak transcription	HUVEC	blood vessel
10	chr6:34555400-34574200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:34555600-34569200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:34555800-34565400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:34556000-34563800	Weak transcription	Stomach Mucosa	stomach
14	chr6:34556200-34612200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:34556400-34563600	Weak transcription	Gastric	stomach
16	chr6:34557200-34573600	Weak transcription	Colonic Mucosa	Colon
17	chr6:34557400-34565000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:34557400-34612400	Weak transcription	Fetal Kidney	kidney
19	chr6:34557600-34563600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:34557600-34563600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:34557600-34565200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:34557600-34565600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:34557600-34566600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr6:34557600-34567200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:34557600-34569000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr6:34557600-34569200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr6:34557600-34569600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:34557600-34569600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:34557600-34573200	Weak transcription	Spleen	Spleen
30	chr6:34557600-34573400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:34557800-34564400	Weak transcription	Brain Hippocampus Middle	brain
32	chr6:34557800-34565200	Weak transcription	Esophagus	oesophagus
33	chr6:34557800-34565800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:34557800-34566000	Weak transcription	Fetal Lung	lung
35	chr6:34557800-34566400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr6:34558000-34563600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:34558000-34568600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:34558000-34570000	Weak transcription	Fetal Intestine Large	intestine
39	chr6:34558000-34573400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:34558000-34573400	Weak transcription	Placenta	Placenta
41	chr6:34558200-34566600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr6:34558200-34568400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr6:34558200-34571600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr6:34558400-34563200	Weak transcription	NHDF-Ad	bronchial
45	chr6:34558400-34565600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr6:34558400-34577200	Weak transcription	Hela-S3	cervix
47	chr6:34558600-34566200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:34558600-34566600	Weak transcription	Dnd41	blood
49	chr6:34558600-34566800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:34558600-34569000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links