Variant report

Variant	rs6687424
Chromosome Location	chr1:224711931-224711932
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:224711904-224711954	HEK293	kidney:	embryo
2	chr1:224711904-224711954	BJ	skin:	n/a
3	chr1:224711904-224711954	Hepatocyte	liver:	n/a
4	chr1:224711904-224711954	A549	lung:	n/a
5	chr1:224711904-224711954	T-47D	breast:	n/a
6	chr1:224711904-224711954	AG10803	skin:	n/a
7	chr1:224711904-224711954	HUVEC	blood vessel:	n/a
8	chr1:224711904-224711954	GM06990	blood:	n/a
9	chr1:224711904-224711954	CMK	blood:	n/a
10	chr1:224711904-224711954	ECC-1	luminal epithelium:	n/a
11	chr1:224711904-224711954	GM12891	blood:	n/a
12	chr1:224711904-224711954	HCF	heart:	n/a
13	chr1:224711904-224711954	HCPEpiC	choroid plexus:	n/a
14	chr1:224711904-224711954	HAEpiC	amniotic membrane:	n/a
15	chr1:224711904-224711954	SK-N-SH_RA	brain:	n/a
16	chr1:224711904-224711954	AG09319	gingival:	n/a
17	chr1:224711904-224711954	HRCEpiC	kidney:	n/a
18	chr1:224711904-224711954	AG04449	skin:	fetal
19	chr1:224711904-224711954	ovcar-3	ovarian:	n/a
20	chr1:224711904-224711954	MCF10A-Er-Src	breast:	n/a
21	chr1:224711904-224711954	SKMC	muscle:	n/a
22	chr1:224711904-224711954	AG04450	lung:	fetal
23	chr1:224711904-224711954	NB4	blood:	n/a
24	chr1:224711904-224711954	HCT-116	colon:	n/a
25	chr1:224711904-224711954	HL-60	blood:	n/a
26	chr1:224711904-224711954	Hela-S3	cervix:	n/a
27	chr1:224711904-224711954	ProgFib	skin:	n/a
28	chr1:224711904-224711954	K562	blood:	n/a
29	chr1:224711904-224711954	HEEpiC	esophagus:	n/a
30	chr1:224711904-224711954	HMEC	breast:	n/a
31	chr1:224711904-224711954	RPTEC	kidney:	n/a
32	chr1:224711904-224711954	AoSMC	blood vessel:	n/a
33	chr1:224711904-224711954	LNCaP	prostate:	n/a
34	chr1:224711904-224711954	PFSK-1	brain:	n/a
35	chr1:224711904-224711954	NHBE	bronchial:	n/a
36	chr1:224711904-224711954	GM12878	blood:	n/a
37	chr1:224711904-224711954	MCF-7	breast:	n/a
38	chr1:224711904-224711954	HepG2	liver:	n/a
39	chr1:224711904-224711954	HPAEpiC	pulmonary alveolar:	n/a
40	chr1:224711904-224711954	H1-hESC	embryonic stem cell:	embryo
41	chr1:224711904-224711954	IMR90	lung:	fetal
42	chr1:224711904-224711954	HIPEpiC	eye:	n/a
43	chr1:224711904-224711954	SK-N-MC	brain:	n/a
44	chr1:224711904-224711954	BE2_C	brain:	n/a
45	chr1:224711904-224711954	GM12892	blood:	n/a
46	chr1:224711904-224711954	GM19239	blood:	n/a
47	chr1:224711904-224711954	Caco-2	colon:	n/a
48	chr1:224711904-224711954	NH-A	brain:	n/a
49	chr1:224711904-224711954	Jurkat	blood:	n/a
50	chr1:224711904-224711954	NHDF-neo	bronchial:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:224690598..224692730-chr1:224711571..224713777,2	K562	blood:
2	chr1:224688210..224692730-chr1:224708810..224713777,4	K562	blood:
3	chr1:224710212..224713081-chr1:224713439..224718484,6	K562	blood:
4	chr1:224705243..224707565-chr1:224710665..224712666,2	K562	blood:
5	chr1:224710212..224711959-chr1:224715661..224718484,2	K562	blood:
6	chr1:224711921..224714079-chr1:224715573..224717114,2	MCF-7	breast:

No data

Variant related genes	Relation type
CNIH3	CpG island
ENSG00000143786	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10495221	1.00[EUR][1000 genomes]
rs11801211	1.00[EUR][1000 genomes]
rs11802182	1.00[EUR][1000 genomes]
rs11807149	1.00[EUR][1000 genomes]
rs11809688	1.00[EUR][1000 genomes]
rs11809710	1.00[EUR][1000 genomes]
rs11810160	1.00[EUR][1000 genomes]
rs11811935	1.00[EUR][1000 genomes]
rs11812007	1.00[EUR][1000 genomes]
rs13374584	1.00[EUR][1000 genomes]
rs13376231	1.00[AMR][1000 genomes]
rs13376387	1.00[YRI][hapmap]
rs1499284	1.00[EUR][1000 genomes]
rs16846190	1.00[EUR][1000 genomes]
rs16846212	1.00[EUR][1000 genomes]
rs16846293	1.00[EUR][1000 genomes]
rs16846494	1.00[EUR][1000 genomes]
rs16847675	1.00[EUR][1000 genomes]
rs16847784	1.00[EUR][1000 genomes]
rs16847858	1.00[EUR][1000 genomes]
rs16847870	1.00[EUR][1000 genomes]
rs16847871	1.00[EUR][1000 genomes]
rs16849419	1.00[EUR][1000 genomes]
rs16849547	1.00[EUR][1000 genomes]
rs1857042	1.00[EUR][1000 genomes]
rs2068945	1.00[EUR][1000 genomes]
rs2794805	1.00[EUR][1000 genomes]
rs4653586	1.00[EUR][1000 genomes]
rs55712053	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57469223	1.00[EUR][1000 genomes]
rs57719044	1.00[EUR][1000 genomes]
rs57967341	1.00[EUR][1000 genomes]
rs58304668	1.00[EUR][1000 genomes]
rs58649883	1.00[EUR][1000 genomes]
rs58788859	1.00[EUR][1000 genomes]
rs58814229	1.00[EUR][1000 genomes]
rs59034185	1.00[EUR][1000 genomes]
rs59577766	1.00[EUR][1000 genomes]
rs59710928	1.00[EUR][1000 genomes]
rs60349703	1.00[EUR][1000 genomes]
rs60544953	1.00[AMR][1000 genomes]
rs60627429	1.00[EUR][1000 genomes]
rs60715845	1.00[EUR][1000 genomes]
rs60831135	1.00[EUR][1000 genomes]
rs61000820	1.00[EUR][1000 genomes]
rs61155217	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61278437	1.00[EUR][1000 genomes]
rs6658918	1.00[EUR][1000 genomes]
rs6659109	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6674133	1.00[EUR][1000 genomes]
rs6681611	1.00[EUR][1000 genomes]
rs6691181	1.00[EUR][1000 genomes]
rs6702649	1.00[EUR][1000 genomes]
rs6702972	1.00[EUR][1000 genomes]
rs73121865	1.00[EUR][1000 genomes]
rs73123788	1.00[EUR][1000 genomes]
rs73123791	1.00[EUR][1000 genomes]
rs73125526	1.00[EUR][1000 genomes]
rs73125529	1.00[EUR][1000 genomes]
rs73133345	1.00[EUR][1000 genomes]
rs74146264	1.00[EUR][1000 genomes]
rs74146368	1.00[AMR][1000 genomes]
rs74146372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74146374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74146377	1.00[EUR][1000 genomes]
rs74146381	1.00[EUR][1000 genomes]
rs74146382	1.00[EUR][1000 genomes]
rs74146383	1.00[EUR][1000 genomes]
rs74146384	1.00[EUR][1000 genomes]
rs74146386	1.00[EUR][1000 genomes]
rs74146389	1.00[EUR][1000 genomes]
rs7512165	1.00[EUR][1000 genomes]
rs9661679	1.00[EUR][1000 genomes]
rs9661938	1.00[EUR][1000 genomes]
rs985300	0.85[AFR][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224694200-224717600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:224694200-224727600	Weak transcription	Brain Anterior Caudate	brain
3	chr1:224696400-224716600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:224701800-224716600	Weak transcription	Ovary	ovary
5	chr1:224702000-224716600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:224702200-224716600	Weak transcription	Dnd41	blood
7	chr1:224705200-224713600	Weak transcription	Fetal Brain Male	brain
8	chr1:224708400-224712000	Weak transcription	HSMM	muscle
9	chr1:224709000-224714200	Enhancers	NHDF-Ad	bronchial
10	chr1:224709200-224713400	Enhancers	HMEC	breast
11	chr1:224709400-224712800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:224710200-224712600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:224710400-224713200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:224710400-224713800	Enhancers	NH-A	brain
15	chr1:224710600-224712000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:224710600-224712000	Weak transcription	NHEK	skin
17	chr1:224710600-224716600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:224710800-224713000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:224711200-224714000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:224711200-224720400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:224711400-224713800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:224711600-224712000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:224711800-224713800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:224711800-224713800	Enhancers	Osteobl	bone
25	chr1:224711800-224716600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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