Variant report

Variant	rs853422
Chromosome Location	chr6:4134031-4134032
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr6:4133974-4134286	T-47D	breast:	n/a	n/a
2	GATA3	chr6:4134018-4134372	T-47D	breast:	n/a	n/a
3	GATA3	chr6:4133968-4134387	T-47D	breast:	n/a	n/a
4	TEAD4	chr6:4134014-4135039	K562	blood:	n/a	n/a
5	IRF1	chr6:4133973-4135818	K562	blood:	n/a	chr6:4135177-4135190 chr6:4134990-4135001 chr6:4135178-4135192 chr6:4134988-4135001 chr6:4135178-4135190 chr6:4135178-4135191 chr6:4135178-4135191 chr6:4135179-4135193 chr6:4135178-4135189 chr6:4134988-4135001 chr6:4135177-4135197 chr6:4135178-4135191 chr6:4135178-4135191 chr6:4134936-4134952
6	UBTF	chr6:4134026-4135847	K562	blood:	n/a	n/a
7	RFX5	chr6:4133781-4134646	HepG2	liver:	n/a	n/a
8	MXI1	chr6:4133783-4136945	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:4056059..4057941-chr6:4133460..4135296,2	K562	blood:
2	chr6:4016355..4024618-chr6:4131840..4138381,21	K562	blood:
3	chr6:4017302..4025509-chr6:4131840..4138381,19	K562	blood:

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

Variant related genes	Relation type
ECI2	TF binding region
ENSG00000254821	TF binding region
ENSG00000234817	TF binding region
ENSG00000272248	Chromatin interaction
ENSG00000112739	Chromatin interaction
ENSG00000230648	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10085196	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1204950	0.93[ASN][1000 genomes]
rs13205642	0.88[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs13206444	0.89[EUR][1000 genomes]
rs13210282	1.00[ASW][hapmap];0.88[CEU][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2326407	0.89[EUR][1000 genomes]
rs34094324	0.89[EUR][1000 genomes]
rs34200917	0.89[EUR][1000 genomes]
rs583807	0.82[JPT][hapmap]
rs590182	0.82[JPT][hapmap]
rs605301	1.00[ASN][1000 genomes]
rs608917	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611677	0.95[ASN][1000 genomes]
rs622859	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625577	1.00[ASN][1000 genomes]
rs627902	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629533	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs633677	1.00[ASN][1000 genomes]
rs638329	0.83[ASW][hapmap];0.86[YRI][hapmap]
rs653674	0.82[JPT][hapmap]
rs656694	1.00[ASN][1000 genomes]
rs6597030	0.88[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs715165	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs71553906	0.89[EUR][1000 genomes]
rs7742642	0.84[EUR][1000 genomes]
rs853412	0.98[ASN][1000 genomes]
rs853421	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328222	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]
rs945251	0.93[ASN][1000 genomes]
rs9689605	0.88[CEU][hapmap];1.00[TSI][hapmap];0.89[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
rs853422	FOXF2	cis	cerebellum	SCAN
rs853422	PRPF4B	cis	parietal	SCAN
rs853422	F13A1	cis	parietal	SCAN

Chromatin state (count:125 , 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	chr6:4127000-4134200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:4127000-4134200	Weak transcription	Aorta	Aorta
5	chr6:4127200-4134200	Weak transcription	HMEC	breast
6	chr6:4129400-4134400	Weak transcription	Lung	lung
7	chr6:4131000-4134200	Weak transcription	HSMMtube	muscle
8	chr6:4131200-4134200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr6:4131200-4134200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:4131200-4134200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:4131200-4134400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr6:4132400-4134200	Weak transcription	Colonic Mucosa	Colon
13	chr6:4132600-4134200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:4132600-4134200	Weak transcription	Gastric	stomach
15	chr6:4132600-4134200	Weak transcription	Psoas Muscle	Psoas
16	chr6:4132600-4134200	Weak transcription	Small Intestine	intestine
17	chr6:4132600-4134200	Weak transcription	HSMM	muscle
18	chr6:4132600-4134400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:4132600-4134400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:4132600-4134400	Weak transcription	Esophagus	oesophagus
21	chr6:4132600-4134400	Weak transcription	Right Ventricle	heart
22	chr6:4132800-4134200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:4132800-4134200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:4132800-4134200	Weak transcription	Primary B cells from cord blood	blood
25	chr6:4132800-4134200	Weak transcription	Fetal Kidney	kidney
26	chr6:4132800-4134200	Weak transcription	Fetal Muscle Leg	muscle
27	chr6:4132800-4134200	Weak transcription	Placenta	Placenta
28	chr6:4132800-4134200	Weak transcription	Left Ventricle	heart
29	chr6:4132800-4134200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:4133000-4134200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:4133000-4134400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr6:4133200-4134200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:4133200-4134200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr6:4133200-4134200	Weak transcription	Primary T cells from cord blood	blood
35	chr6:4133200-4134200	Enhancers	Brain Hippocampus Middle	brain
36	chr6:4133200-4134200	Weak transcription	Fetal Thymus	thymus
37	chr6:4133200-4134400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:4133200-4134800	Flanking Active TSS	Liver	Liver
39	chr6:4133400-4134200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr6:4133400-4134200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:4133400-4134200	Weak transcription	Fetal Stomach	stomach
42	chr6:4133400-4134200	Weak transcription	Pancreas	Pancrea
43	chr6:4133400-4134200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr6:4133400-4134200	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr6:4133400-4134400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:4133600-4134200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:4133600-4134200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr6:4133600-4134400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr6:4133600-4134400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:4133600-4134400	Enhancers	Fetal Brain Male	brain

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