Variant report

Variant	rs6597031
Chromosome Location	chr6:4106370-4106371
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4101330..4103030-chr6:4105237..4107342,2	K562	blood:
2	chr6:4101330..4103271-chr6:4104931..4106737,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11751668	0.82[JPT][hapmap]
rs11753305	0.87[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2783073	0.94[EUR][1000 genomes]
rs584585	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs612022	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs613260	0.93[EUR][1000 genomes]
rs613709	0.93[EUR][1000 genomes]
rs617790	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs619873	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs620484	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs629362	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs633290	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs634698	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs643232	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs649725	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs659025	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs659305	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs660560	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs676683	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs689308	0.92[EUR][1000 genomes]
rs6932036	0.80[ASN][1000 genomes]
rs6935587	0.83[JPT][hapmap]
rs7166	1.00[CEU][hapmap];0.80[JPT][hapmap];0.94[EUR][1000 genomes]
rs7744628	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs7757606	0.93[EUR][1000 genomes]
rs853416	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs853417	0.94[EUR][1000 genomes]
rs9328220	0.93[EUR][1000 genomes]
rs9378843	0.81[ASN][1000 genomes]
rs9392556	0.82[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs9503936	0.80[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6597031	ECI2	cis	Thyroid	GTEx
rs6597031	C6orf201	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4101800-4110200	Weak transcription	Stomach Mucosa	stomach
2	chr6:4102600-4113800	Weak transcription	Psoas Muscle	Psoas
3	chr6:4103400-4109800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:4103400-4110000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:4103400-4115400	Weak transcription	Fetal Brain Male	brain
6	chr6:4103400-4115600	Weak transcription	Fetal Stomach	stomach
7	chr6:4103400-4115600	Weak transcription	Gastric	stomach
8	chr6:4103800-4108400	Weak transcription	Fetal Intestine Small	intestine
9	chr6:4104400-4108400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:4104400-4109200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:4104600-4108800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:4104600-4115600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:4104600-4115600	Weak transcription	Pancreas	Pancrea
14	chr6:4104800-4115000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:4104800-4115200	Weak transcription	HMEC	breast
16	chr6:4105000-4113600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:4105400-4111000	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links