Variant report

Variant	rs16890651
Chromosome Location	chr5:61629539-61629540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61622184..61624632-chr5:61629178..61631603,3	K562	blood:
2	chr5:61622009..61624604-chr5:61628091..61630897,2	K562	blood:
3	chr5:61601551..61603315-chr5:61628509..61630396,2	MCF-7	breast:
4	chr5:61601235..61603085-chr5:61628618..61631390,2	K562	blood:
5	chr5:61627722..61630548-chr5:61641622..61644001,2	MCF-7	breast:
6	chr5:61561395..61563266-chr5:61628626..61630582,2	K562	blood:

Variant related genes	Relation type
ENSG00000068796	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1108158	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11740652	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742167	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11747516	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13155253	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13156073	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13156695	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13161789	0.87[AMR][1000 genomes]
rs13162519	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13163533	0.86[EUR][1000 genomes]
rs13169321	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13170425	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13174779	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13176923	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13178729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13181377	0.87[AMR][1000 genomes]
rs13189446	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13190153	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs153860	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs153864	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs153866	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs153869	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs153873	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs16875037	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890613	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16890618	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890634	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17382217	1.00[CEU][hapmap]
rs2059162	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2063255	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2272291	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2441115	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs246198	0.82[ASN][1000 genomes]
rs255391	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs26626	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs26627	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs27090	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs32047	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs32178	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs32180	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs32184	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs32185	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs34220654	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34596001	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35011	1.00[CEU][hapmap]
rs35012	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs35058	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs35238667	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35311093	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35572300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35672643	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35699711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35744020	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35746052	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35794032	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35808056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35815430	0.96[EUR][1000 genomes]
rs35842742	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36105063	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3776612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822487	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs40290	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs4289514	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71617425	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71617426	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71617427	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71617428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71617429	0.88[EUR][1000 genomes]
rs7446543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814169	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs971965	0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2757996	chr5:61403138-61687817	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv881726	chr5:61556730-61676911	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv881727	chr5:61578041-61700970	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv1033578	chr5:61606610-61911153	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv1025145	chr5:61624735-61824265	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1029708	chr5:61625813-61877628	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16890651	KIF2A	Cis_1M	lymphoblastoid	RTeQTL
rs16890651	EGR4	trans	brain	seeQTL
rs16890651	ARC	trans	brain	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61603400-61658600	Weak transcription	Aorta	Aorta
2	chr5:61604400-61643800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:61604600-61630000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:61604600-61658600	Weak transcription	Fetal Kidney	kidney
5	chr5:61607800-61669400	Weak transcription	NHLF	lung
6	chr5:61610200-61658600	Weak transcription	Ovary	ovary
7	chr5:61611600-61630200	Weak transcription	Fetal Intestine Large	intestine
8	chr5:61611600-61639000	Weak transcription	HMEC	breast
9	chr5:61611600-61643800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr5:61611800-61630000	Weak transcription	NHEK	skin
11	chr5:61612000-61642400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr5:61612000-61661000	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:61615600-61658600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:61618200-61629600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:61618200-61647800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr5:61618400-61658600	Weak transcription	Hela-S3	cervix
17	chr5:61619200-61630000	Weak transcription	Colonic Mucosa	Colon
18	chr5:61621600-61631600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:61621800-61638000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:61622400-61633400	Weak transcription	HUVEC	blood vessel
21	chr5:61622400-61676000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:61622600-61643800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr5:61622600-61658800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr5:61623000-61643000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr5:61623000-61646200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr5:61623800-61643800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr5:61623800-61658600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:61624000-61669600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:61625400-61644000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:61625400-61646200	Weak transcription	Adipose Nuclei	Adipose
31	chr5:61626000-61629600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:61626600-61631800	Weak transcription	A549	lung
33	chr5:61626600-61639000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:61627000-61630200	Enhancers	Fetal Brain Male	brain
35	chr5:61627000-61631000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr5:61628000-61629600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr5:61628000-61638000	Weak transcription	Small Intestine	intestine
38	chr5:61628200-61629600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:61628200-61630200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:61628200-61644400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:61628400-61629800	Enhancers	Brain Hippocampus Middle	brain
42	chr5:61628400-61630800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:61628600-61631200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:61628800-61630000	Enhancers	Fetal Heart	heart
45	chr5:61628800-61630200	Enhancers	Brain Angular Gyrus	brain
46	chr5:61628800-61630400	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr5:61628800-61631800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr5:61628800-61632000	Strong transcription	Dnd41	blood
49	chr5:61628800-61652000	Weak transcription	Fetal Brain Female	brain
50	chr5:61629000-61629600	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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