Variant report

Variant	rs6686341
Chromosome Location	chr1:76505266-76505267
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10493580	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10873865	0.89[AFR][1000 genomes]
rs11162070	0.90[ASN][1000 genomes]
rs11162073	0.88[ASN][1000 genomes]
rs11804459	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11805321	0.90[ASN][1000 genomes]
rs12032833	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12032853	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12033420	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038667	0.90[ASN][1000 genomes]
rs12039427	0.90[ASN][1000 genomes]
rs12040748	0.90[ASN][1000 genomes]
rs12040836	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045798	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1340690	0.81[AFR][1000 genomes]
rs1344929	0.97[EUR][1000 genomes]
rs1370714	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17599859	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1934816	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4083965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4146895	0.82[ASN][1000 genomes]
rs4146896	0.82[ASN][1000 genomes]
rs4949690	0.90[ASN][1000 genomes]
rs5022490	0.89[AFR][1000 genomes]
rs59862803	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61771303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679705	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685661	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688109	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692421	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696470	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703050	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703053	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703146	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7513692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517793	0.90[ASN][1000 genomes]
rs7517974	0.90[ASN][1000 genomes]
rs7529565	0.90[ASN][1000 genomes]
rs7536325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2754129	chr1:76489579-76529279	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv870968	chr1:76490234-76552475	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6686341	MSH4	cis	parietal	SCAN
rs6686341	RABGGTB	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76502200-76507200	Enhancers	Fetal Intestine Large	intestine
2	chr1:76502200-76507400	Enhancers	Fetal Intestine Small	intestine
3	chr1:76503400-76505800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:76503400-76505800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:76503400-76507000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:76503600-76505800	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr1:76503600-76509600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:76504000-76509200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:76504200-76505800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:76504200-76506000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:76504200-76506000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:76504200-76506200	Weak transcription	Fetal Lung	lung
13	chr1:76504200-76506600	Weak transcription	Fetal Stomach	stomach
14	chr1:76504200-76507400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:76504400-76505800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:76504400-76506000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:76504400-76506200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:76504800-76505800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:76504800-76505800	Weak transcription	Fetal Kidney	kidney
20	chr1:76505000-76505600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:76505000-76506000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:76505200-76505600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:76505200-76506000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:76505200-76506200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:76505200-76506200	Weak transcription	Rectal Mucosa Donor 29	rectum

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