Variant report

Variant	rs3934540
Chromosome Location	chr4:7822450-7822451
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7822325..7824045-chr4:7827904..7830215,2	K562	blood:
2	chr4:7821478..7824762-chr4:7830984..7832919,3	K562	blood:
3	chr4:7822325..7825462-chr4:7828397..7830973,3	K562	blood:
4	chr4:7818745..7823196-chr4:7823235..7826855,4	K562	blood:

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10009045	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10018256	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10049998	1.00[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap]
rs11932843	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs12639946	0.89[CEU][hapmap]
rs13115701	0.85[ASN][1000 genomes]
rs13131154	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs13137140	0.85[ASN][1000 genomes]
rs13140004	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs13145572	0.85[ASN][1000 genomes]
rs13146302	0.85[ASN][1000 genomes]
rs1320073	0.85[ASN][1000 genomes]
rs17770147	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs17770177	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2067842	0.89[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2385902	0.88[CHB][hapmap]
rs28394221	0.85[ASN][1000 genomes]
rs28539821	0.85[ASN][1000 genomes]
rs28546404	0.85[ASN][1000 genomes]
rs28605531	0.85[ASN][1000 genomes]
rs28613311	0.82[ASN][1000 genomes]
rs28631977	0.80[ASN][1000 genomes]
rs28673208	0.85[ASN][1000 genomes]
rs28688265	0.85[ASN][1000 genomes]
rs28754920	0.85[ASN][1000 genomes]
rs2891927	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs34072304	0.80[ASN][1000 genomes]
rs34075381	0.85[ASN][1000 genomes]
rs34092549	0.85[ASN][1000 genomes]
rs34119140	0.80[ASN][1000 genomes]
rs34121576	0.85[ASN][1000 genomes]
rs34132874	0.80[ASN][1000 genomes]
rs34181918	0.85[ASN][1000 genomes]
rs34189407	0.85[ASN][1000 genomes]
rs34221000	0.85[ASN][1000 genomes]
rs34383852	0.85[ASN][1000 genomes]
rs34392913	0.85[ASN][1000 genomes]
rs34570748	0.84[ASN][1000 genomes]
rs34598003	0.80[ASN][1000 genomes]
rs34652148	0.85[ASN][1000 genomes]
rs34712341	0.85[ASN][1000 genomes]
rs34868842	0.85[ASN][1000 genomes]
rs34909423	0.80[ASN][1000 genomes]
rs34982807	0.80[ASN][1000 genomes]
rs35138920	0.85[ASN][1000 genomes]
rs35152796	0.85[ASN][1000 genomes]
rs35154266	0.85[ASN][1000 genomes]
rs35238070	0.85[ASN][1000 genomes]
rs35349192	0.85[ASN][1000 genomes]
rs35502845	0.85[ASN][1000 genomes]
rs35727635	0.85[ASN][1000 genomes]
rs35735994	0.85[ASN][1000 genomes]
rs35881667	0.84[ASN][1000 genomes]
rs35905776	0.85[ASN][1000 genomes]
rs35967175	0.85[ASN][1000 genomes]
rs36013696	0.85[ASN][1000 genomes]
rs36046241	0.81[ASN][1000 genomes]
rs36106793	0.85[ASN][1000 genomes]
rs4234831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs4256209	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs4296663	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs4361385	0.89[CHB][hapmap];0.80[CHD][hapmap];0.80[ASN][1000 genomes]
rs4411970	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs4443285	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4447865	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4487321	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4579115	0.89[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4689860	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4689865	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4689875	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696742	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4696747	0.84[ASN][1000 genomes]
rs4696762	0.85[ASN][1000 genomes]
rs4696772	1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs62289341	0.83[ASN][1000 genomes]
rs62289351	0.83[ASN][1000 genomes]
rs6446624	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446625	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446627	0.90[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6446629	0.80[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6824266	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs6826598	0.81[ASN][1000 genomes]
rs6828574	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs6828858	0.91[EUR][1000 genomes]
rs6829505	0.85[ASN][1000 genomes]
rs6829710	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6832352	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs6833054	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs6837845	0.85[ASN][1000 genomes]
rs6838055	0.85[ASN][1000 genomes]
rs6845014	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs6855982	0.85[ASN][1000 genomes]
rs6856371	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6856795	0.94[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71600561	0.81[ASN][1000 genomes]
rs71601887	0.85[ASN][1000 genomes]
rs71601888	0.85[ASN][1000 genomes]
rs71601889	0.85[ASN][1000 genomes]
rs71601890	0.85[ASN][1000 genomes]
rs71601892	0.85[ASN][1000 genomes]
rs71612280	0.81[EUR][1000 genomes]
rs7654361	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7660568	0.85[ASN][1000 genomes]
rs7672185	0.80[EUR][1000 genomes]
rs7682202	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7682611	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7684718	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7691386	0.85[ASN][1000 genomes]
rs7697255	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs9996019	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS 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	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active 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	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
6	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription 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	6 gene(s)	inside rSNPs	diseases
7	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3934540	AFAP	cis	multi-tissue	Pritchard
rs3934540	CRMP1	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:7787000-7829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr4:7791000-7829400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr4:7800600-7828800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:7804000-7829200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:7805200-7822600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:7806400-7824600	Weak transcription	Fetal Thymus	thymus
8	chr4:7808000-7823000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:7808600-7830000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:7809600-7823000	Weak transcription	Brain Angular Gyrus	brain
11	chr4:7809600-7828000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:7809800-7823400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr4:7809800-7823400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:7810000-7823400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:7813400-7825200	Weak transcription	Right Ventricle	heart
16	chr4:7813400-7829800	Weak transcription	Spleen	Spleen
17	chr4:7814200-7823000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr4:7814400-7823800	Weak transcription	Stomach Mucosa	stomach
19	chr4:7814400-7826600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:7814600-7822600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:7814600-7822600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr4:7814600-7824800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:7814800-7829800	Genic enhancers	Osteobl	bone
24	chr4:7816400-7823000	Strong transcription	HSMM	muscle
25	chr4:7816600-7824800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:7817000-7823800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:7817600-7823200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:7817800-7823400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:7818000-7822600	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr4:7818000-7830000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:7818200-7829400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:7818400-7823600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:7818800-7823000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:7818800-7823400	Weak transcription	Psoas Muscle	Psoas
35	chr4:7818800-7825200	Weak transcription	Gastric	stomach
36	chr4:7818800-7828200	Weak transcription	Hela-S3	cervix
37	chr4:7819200-7823400	Weak transcription	Fetal Kidney	kidney
38	chr4:7819400-7822600	Genic enhancers	Stomach Smooth Muscle	stomach
39	chr4:7819600-7823200	Genic enhancers	Fetal Muscle Leg	muscle
40	chr4:7819600-7824000	Genic enhancers	Fetal Stomach	stomach
41	chr4:7819600-7826600	Enhancers	Fetal Heart	heart
42	chr4:7819800-7822600	Strong transcription	Colonic Mucosa	Colon
43	chr4:7819800-7823200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:7819800-7823200	Genic enhancers	Fetal Muscle Trunk	muscle
45	chr4:7819800-7823400	Enhancers	Ovary	ovary
46	chr4:7819800-7823800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr4:7819800-7825000	Genic enhancers	Fetal Intestine Small	intestine
48	chr4:7819800-7834400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:7820000-7823200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr4:7820000-7823400	Genic enhancers	Rectal Mucosa Donor 31	rectum

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