Variant report

Variant	rs6698343
Chromosome Location	chr1:224680332-224680333
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224677828..224680425-chr1:224681329..224683166,2	K562	blood:
2	chr1:224663142..224665952-chr1:224678882..224681699,2	K562	blood:
3	chr1:224640045..224642435-chr1:224680202..224683058,2	MCF-7	breast:
4	chr1:224679447..224681226-chr1:224689931..224692404,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10159333	0.86[EUR][1000 genomes]
rs10495219	0.85[EUR][1000 genomes]
rs10753467	0.89[EUR][1000 genomes]
rs10753468	0.89[EUR][1000 genomes]
rs10916614	0.84[EUR][1000 genomes]
rs10916616	0.86[EUR][1000 genomes]
rs10916617	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10916619	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11577170	0.89[EUR][1000 genomes]
rs11578709	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584057	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584638	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11588973	0.88[EUR][1000 genomes]
rs11590658	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11800613	0.89[EUR][1000 genomes]
rs11805973	0.82[EUR][1000 genomes]
rs11807763	0.85[EUR][1000 genomes]
rs12062871	0.90[EUR][1000 genomes]
rs12731630	0.89[EUR][1000 genomes]
rs12738799	0.85[EUR][1000 genomes]
rs12739486	0.85[EUR][1000 genomes]
rs12742989	0.86[EUR][1000 genomes]
rs12743200	0.89[EUR][1000 genomes]
rs12747286	0.83[EUR][1000 genomes]
rs12751161	0.85[EUR][1000 genomes]
rs12755338	0.85[EUR][1000 genomes]
rs12758302	0.81[EUR][1000 genomes]
rs12758579	0.89[EUR][1000 genomes]
rs1544196	0.88[EUR][1000 genomes]
rs16848365	0.89[EUR][1000 genomes]
rs17570292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185684	0.89[EUR][1000 genomes]
rs28434172	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2897048	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34791963	0.83[EUR][1000 genomes]
rs35011635	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35067427	0.89[EUR][1000 genomes]
rs35277713	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35303987	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35365551	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35571080	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35767322	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35804313	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35915186	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653587	0.86[EUR][1000 genomes]
rs55730749	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6426123	0.86[EUR][1000 genomes]
rs6426125	0.86[EUR][1000 genomes]
rs6426126	0.86[EUR][1000 genomes]
rs66467176	0.88[EUR][1000 genomes]
rs66530931	0.90[EUR][1000 genomes]
rs6663522	0.89[EUR][1000 genomes]
rs6678608	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71644786	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7365151	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7514575	0.84[EUR][1000 genomes]
rs7527044	0.84[EUR][1000 genomes]
rs7529310	0.86[EUR][1000 genomes]
rs867362	0.89[EUR][1000 genomes]
rs885606	0.89[EUR][1000 genomes]
rs9970697	0.88[EUR][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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS 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 miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6698343	CNIH4	cis	Thyroid	GTEx
rs6698343	CNIH4	cis	Nerve Tibial	GTEx
rs6698343	CNIH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224677200-224680800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:224677200-224685000	Weak transcription	NHLF	lung
3	chr1:224677400-224680400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:224677400-224681000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:224677600-224680400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:224677600-224682600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:224677600-224683400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:224677800-224683400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:224677800-224684800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:224677800-224684800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:224677800-224685400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:224678000-224680400	Weak transcription	NHDF-Ad	bronchial
13	chr1:224678000-224683000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr1:224678200-224680600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:224678200-224683200	Weak transcription	Osteobl	bone
16	chr1:224678800-224680400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:224678800-224682600	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:224679200-224683400	Weak transcription	HSMM	muscle
19	chr1:224679800-224689600	Weak transcription	Pancreas	Pancrea
20	chr1:224680000-224681000	Weak transcription	Fetal Intestine Small	intestine
21	chr1:224680000-224683000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr1:224680000-224685600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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