Variant report

Variant	rs4654122
Chromosome Location	chr1:246780557-246780558
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246779828..246782694-chr1:246783827..246786516,2	K562	blood:
2	chr1:246775147..246776815-chr1:246778943..246781797,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10754528	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10754530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10924785	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006082	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3006085	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007401	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3007405	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3007406	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3124075	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3124077	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3124078	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3124079	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3124084	0.90[ASN][1000 genomes]
rs3129542	0.90[ASN][1000 genomes]
rs3129544	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3129546	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3129547	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3129549	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3129552	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3129553	0.81[ASN][1000 genomes]
rs3129557	0.86[ASN][1000 genomes]
rs3129583	0.95[ASN][1000 genomes]
rs4129249	0.80[MEX][hapmap]
rs4654123	0.89[ASN][1000 genomes]
rs72762785	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7520403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9426203	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9426250	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9426251	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004119	chr1:245957145-246813150	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv535389	chr1:245957145-246813150	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1014529	chr1:245957145-246817877	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv868852	chr1:245969229-246811220	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv948348	chr1:246090818-246853200	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv430402	chr1:246124959-246787448	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1013800	chr1:246472691-246840960	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv535409	chr1:246472691-246840960	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	esv2762191	chr1:246546436-246815064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv1010453	chr1:246645797-246815052	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv998579	chr1:246666041-246817877	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv1010316	chr1:246686301-246840960	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv535414	chr1:246686301-246840960	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
16	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
17	nsv528615	chr1:246708467-246843315	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
18	nsv1014280	chr1:246709243-246823255	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv1013264	chr1:246723012-246807400	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv535415	chr1:246723012-246807400	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	nsv1005214	chr1:246730885-246841107	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
22	esv3346702	chr1:246769596-246798732	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	esv3368182	chr1:246770638-246799861	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
24	nsv1002595	chr1:246774036-246846548	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv869936	chr1:246778181-246811161	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4654122	SDCCAG8	cis	cerebellum	SCAN
rs4654122	ZNF670	cis	parietal	SCAN
rs4654122	OR1C1	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246739000-246806200	Weak transcription	Aorta	Aorta
2	chr1:246755400-246832800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:246764200-246784200	Weak transcription	Thymus	Thymus
4	chr1:246766200-246784200	Weak transcription	Dnd41	blood
5	chr1:246771400-246784600	Weak transcription	Fetal Stomach	stomach
6	chr1:246772200-246795600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:246772400-246784600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:246772600-246784000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:246772600-246784000	Weak transcription	Liver	Liver
10	chr1:246772600-246784000	Weak transcription	GM12878-XiMat	blood
11	chr1:246772600-246784800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:246772600-246784800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:246772600-246790600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:246772600-246795600	Weak transcription	HepG2	liver
15	chr1:246772800-246783800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:246772800-246783800	Weak transcription	Fetal Intestine Small	intestine
17	chr1:246772800-246784000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:246772800-246784000	Weak transcription	Spleen	Spleen
19	chr1:246772800-246789200	Weak transcription	Ovary	ovary
20	chr1:246773000-246782600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr1:246773000-246784800	Weak transcription	Fetal Muscle Leg	muscle
22	chr1:246773000-246784800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:246773000-246790200	Weak transcription	Small Intestine	intestine
24	chr1:246773000-246790200	Weak transcription	HSMM	muscle
25	chr1:246773000-246792400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:246773200-246780600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:246773200-246782200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:246773200-246799000	Weak transcription	Fetal Lung	lung
29	chr1:246773400-246784400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr1:246773400-246785000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:246773600-246795400	Weak transcription	Placenta	Placenta
32	chr1:246773800-246784600	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:246773800-246795800	Weak transcription	Hela-S3	cervix
34	chr1:246774000-246792600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:246774200-246781000	Weak transcription	Primary T cells from cord blood	blood
36	chr1:246774400-246780600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:246774400-246785600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr1:246774600-246780600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:246774600-246781800	Weak transcription	Fetal Thymus	thymus
40	chr1:246774600-246800400	Weak transcription	Pancreas	Pancrea
41	chr1:246774800-246795600	Weak transcription	Brain Substantia Nigra	brain
42	chr1:246775200-246780600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:246776000-246790000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:246776200-246784000	Weak transcription	Lung	lung
45	chr1:246776400-246790400	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:246776600-246784200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:246776600-246790600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:246776600-246794000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:246776800-246780600	Weak transcription	Brain Anterior Caudate	brain
50	chr1:246776800-246780600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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