Variant report

Variant	rs11734860
Chromosome Location	chr4:7828233-7828234
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	chr4:7822325..7824045-chr4:7827904..7830215,2	K562	blood:
2	chr4:7825242..7828581-chr4:7828624..7832177,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SORCS2-3	chr4:7824831-7831552	refGeneNc_1113_NR_026892

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11721583	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs11721609	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11724632	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11728778	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11729332	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs11729602	0.86[EUR][1000 genomes]
rs11730169	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11731942	0.86[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733311	0.83[EUR][1000 genomes]
rs11734524	0.87[EUR][1000 genomes]
rs11737447	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs11933506	0.85[YRI][hapmap]
rs13103193	1.00[ASN][1000 genomes]
rs13113113	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13117918	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13121514	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13125295	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs13128495	0.82[JPT][hapmap]
rs13132939	0.88[EUR][1000 genomes]
rs17382379	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs17382393	0.86[EUR][1000 genomes]
rs17466895	0.86[EUR][1000 genomes]
rs28684644	0.86[ASN][1000 genomes]
rs28760598	0.86[ASN][1000 genomes]
rs34250310	0.94[EUR][1000 genomes]
rs34352176	0.86[EUR][1000 genomes]
rs34949259	0.94[EUR][1000 genomes]
rs35041036	0.94[EUR][1000 genomes]
rs35161247	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35509185	0.92[EUR][1000 genomes]
rs35515779	0.89[EUR][1000 genomes]
rs35592594	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35617438	0.92[EUR][1000 genomes]
rs35672467	1.00[ASN][1000 genomes]
rs35726835	0.97[ASN][1000 genomes]
rs35870249	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35889107	0.89[EUR][1000 genomes]
rs36020433	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3934645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41264705	0.89[EUR][1000 genomes]
rs4274845	0.82[YRI][hapmap]
rs4443284	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4594724	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689868	1.00[YRI][hapmap]
rs55698135	0.89[EUR][1000 genomes]
rs55740648	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56270003	0.96[EUR][1000 genomes]
rs56352084	0.84[EUR][1000 genomes]
rs58457272	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61036795	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62289276	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62289280	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62291980	0.86[EUR][1000 genomes]
rs62291983	0.87[EUR][1000 genomes]
rs62291984	0.87[EUR][1000 genomes]
rs885260	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs885261	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv522369	chr4:7826824-7831977	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11734860	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:108 , 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	chr4:7808600-7830000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:7813400-7829800	Weak transcription	Spleen	Spleen
8	chr4:7814800-7829800	Genic enhancers	Osteobl	bone
9	chr4:7818000-7830000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:7818200-7829400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:7819800-7834400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:7820800-7828400	Weak transcription	NHEK	skin
13	chr4:7821000-7829200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:7821000-7829200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr4:7821000-7829400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr4:7821000-7829400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:7821000-7830400	Weak transcription	Esophagus	oesophagus
18	chr4:7821200-7859000	Weak transcription	Aorta	Aorta
19	chr4:7821400-7829400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr4:7821400-7829800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:7823400-7829400	Weak transcription	HMEC	breast
22	chr4:7823800-7830200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:7824600-7834600	Genic enhancers	HUVEC	blood vessel
24	chr4:7825200-7828800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr4:7825400-7829400	Weak transcription	Brain Angular Gyrus	brain
26	chr4:7825400-7829800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:7825400-7839400	Weak transcription	Pancreas	Pancrea
28	chr4:7825600-7829400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:7825600-7829400	Weak transcription	Left Ventricle	heart
30	chr4:7825600-7829400	Weak transcription	Right Ventricle	heart
31	chr4:7825600-7830000	Weak transcription	Brain Substantia Nigra	brain
32	chr4:7825600-7830400	Weak transcription	Small Intestine	intestine
33	chr4:7825600-7830600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr4:7825600-7830800	Weak transcription	Psoas Muscle	Psoas
35	chr4:7825600-7852200	Weak transcription	Gastric	stomach
36	chr4:7825800-7829400	Strong transcription	HSMM	muscle
37	chr4:7825800-7829800	Weak transcription	Fetal Brain Female	brain
38	chr4:7825800-7830200	Weak transcription	Fetal Brain Male	brain
39	chr4:7825800-7854200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr4:7826000-7846000	Weak transcription	Stomach Mucosa	stomach
41	chr4:7826200-7829000	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr4:7826200-7829000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:7826200-7829400	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr4:7826200-7829400	Weak transcription	Fetal Thymus	thymus
45	chr4:7826400-7828800	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr4:7826400-7829600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr4:7826400-7829800	Weak transcription	Brain Hippocampus Middle	brain
48	chr4:7826400-7829800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:7826400-7833600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:7826600-7828400	Weak transcription	Ovary	ovary

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