Variant report

Variant	rs9328222
Chromosome Location	chr6:4131482-4131483
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4130992..4133785-chr6:4183388..4185664,2	K562	blood:
2	chr6:4063923..4066758-chr6:4130890..4132765,2	K562	blood:
3	chr6:4113998..4116630-chr6:4130932..4132448,2	K562	blood:
4	chr6:4067620..4070166-chr6:4130566..4132778,2	K562	blood:
5	chr6:4073031..4076036-chr6:4129401..4132460,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf201-5	chr6:4131253-4134818	NONHSAT107321

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10085196	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11759470	0.87[CEU][hapmap];1.00[GIH][hapmap]
rs13196680	0.87[CEU][hapmap];1.00[GIH][hapmap]
rs13197380	0.87[CEU][hapmap]
rs13200044	0.87[CEU][hapmap]
rs13205642	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];1.00[EUR][1000 genomes]
rs13206444	1.00[EUR][1000 genomes]
rs13209389	0.87[CEU][hapmap]
rs13210282	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13210391	0.85[CEU][hapmap]
rs2326407	1.00[EUR][1000 genomes]
rs34094324	1.00[EUR][1000 genomes]
rs34200917	1.00[EUR][1000 genomes]
rs608917	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs622859	0.89[EUR][1000 genomes]
rs627902	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs638329	0.85[YRI][hapmap]
rs6597030	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs715165	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[EUR][1000 genomes]
rs71553906	1.00[EUR][1000 genomes]
rs7742642	0.94[EUR][1000 genomes]
rs853421	0.89[EUR][1000 genomes]
rs853422	0.83[ASW][hapmap];0.88[CEU][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9689605	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];1.00[EUR][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	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	esv2422231	chr6:4100333-4233454	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9328222	PRPF4B	cis	parietal	SCAN
rs9328222	F13A1	cis	parietal	SCAN
rs9328222	FOXF2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4111000-4134200	Weak transcription	Stomach Mucosa	stomach
2	chr6:4113800-4134600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:4114200-4132200	Strong transcription	Primary T cells from cord blood	blood
4	chr6:4114200-4132800	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr6:4114200-4133400	Strong transcription	Stomach Smooth Muscle	stomach
6	chr6:4114400-4131800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:4114400-4132400	Strong transcription	Fetal Thymus	thymus
8	chr6:4114600-4133600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr6:4114800-4132800	Strong transcription	Duodenum Mucosa	Duodenum
10	chr6:4114800-4133400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr6:4115200-4132000	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr6:4115200-4132000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:4115200-4132600	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr6:4115200-4132800	Strong transcription	Left Ventricle	heart
15	chr6:4115200-4133000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr6:4115200-4133800	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:4115400-4133200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:4115400-4133400	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:4115400-4133800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr6:4115600-4132200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:4115600-4132200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:4115600-4132600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
23	chr6:4116200-4132000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:4121200-4132000	Strong transcription	Primary hematopoietic stem cells	blood
25	chr6:4121600-4132200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:4121600-4133200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr6:4121800-4132000	Strong transcription	Fetal Muscle Leg	muscle
28	chr6:4121800-4132400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:4122400-4132200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:4122400-4133800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:4123800-4133400	Strong transcription	Ovary	ovary
32	chr6:4124200-4133200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:4125000-4132200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:4125200-4133400	Strong transcription	Fetal Stomach	stomach
35	chr6:4126000-4132200	Weak transcription	Gastric	stomach
36	chr6:4126400-4132800	Strong transcription	Fetal Kidney	kidney
37	chr6:4126800-4133200	Strong transcription	Adipose Nuclei	Adipose
38	chr6:4126800-4133400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:4127000-4131600	Genic enhancers	Osteobl	bone
40	chr6:4127000-4132200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:4127000-4132200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:4127000-4133600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:4127000-4134200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:4127000-4134200	Weak transcription	Aorta	Aorta
45	chr6:4127200-4132200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:4127200-4134200	Weak transcription	HMEC	breast
47	chr6:4127400-4133800	Strong transcription	Colon Smooth Muscle	Colon
48	chr6:4127800-4132800	Strong transcription	Fetal Intestine Large	intestine
49	chr6:4127800-4133000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:4127800-4133800	Strong transcription	A549	lung

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