Variant report

Variant	rs3867270
Chromosome Location	chr11:74049569-74049570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1044782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1053021	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736795	0.87[ASN][1000 genomes]
rs10793072	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793074	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793075	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793077	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10793078	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10793079	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10793080	0.86[ASN][1000 genomes]
rs10793081	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10898980	0.81[YRI][hapmap]
rs10898981	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10898983	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11236061	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236063	0.83[YRI][hapmap]
rs11236068	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11236071	0.81[YRI][hapmap]
rs11236073	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11236077	0.87[YRI][hapmap]
rs11236087	0.81[ASW][hapmap];0.85[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11236088	0.85[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1145687	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11559629	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1279293	0.81[YRI][hapmap]
rs17132964	0.81[YRI][hapmap]
rs2887119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3168173	0.93[ASN][1000 genomes]
rs35170680	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3741130	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862799	0.93[ASN][1000 genomes]
rs3867268	0.83[ASN][1000 genomes]
rs3867271	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3867272	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs479968	0.88[ASN][1000 genomes]
rs480358	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs486758	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs4944041	0.83[ASN][1000 genomes]
rs4944887	0.83[ASN][1000 genomes]
rs519083	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538103	0.89[ASN][1000 genomes]
rs58950228	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs592644	0.93[ASN][1000 genomes]
rs595798	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596976	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs597729	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs598869	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61902399	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs623065	0.89[ASN][1000 genomes]
rs625632	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs634608	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs637921	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641271	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646047	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs655719	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs657329	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6592557	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs662393	0.82[ASN][1000 genomes]
rs673103	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7120394	0.83[ASN][1000 genomes]
rs7926851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7928036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930193	0.83[ASN][1000 genomes]
rs7934621	0.86[ASN][1000 genomes]
rs7940145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7941916	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7944333	0.80[ASN][1000 genomes]
rs7945908	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7947911	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3867270	SHANK2	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74031200-74071200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:74037000-74055400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:74037200-74050000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr11:74037400-74051600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:74037400-74052200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:74037400-74078800	Weak transcription	Small Intestine	intestine
7	chr11:74037600-74051600	Weak transcription	Brain Angular Gyrus	brain
8	chr11:74037600-74052800	Weak transcription	A549	lung
9	chr11:74037800-74086200	Weak transcription	Brain Anterior Caudate	brain
10	chr11:74038000-74050400	Weak transcription	Gastric	stomach
11	chr11:74038000-74071200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr11:74038000-74077400	Weak transcription	Psoas Muscle	Psoas
13	chr11:74038000-74077600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr11:74038000-74084400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr11:74038200-74050400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr11:74038200-74052800	Weak transcription	Ovary	ovary
17	chr11:74038200-74053600	Weak transcription	Spleen	Spleen
18	chr11:74038200-74058200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:74038200-74065000	Weak transcription	Aorta	Aorta
20	chr11:74038200-74071000	Weak transcription	Fetal Stomach	stomach
21	chr11:74038200-74071400	Weak transcription	Left Ventricle	heart
22	chr11:74038200-74071400	Weak transcription	Lung	lung
23	chr11:74038200-74082000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr11:74038200-74084400	Weak transcription	Colon Smooth Muscle	Colon
25	chr11:74038400-74051800	Weak transcription	Fetal Muscle Leg	muscle
26	chr11:74038400-74052800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr11:74038400-74084400	Weak transcription	Liver	Liver
28	chr11:74038400-74086200	Weak transcription	Adipose Nuclei	Adipose
29	chr11:74038600-74051600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr11:74038600-74071400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr11:74038800-74070600	Weak transcription	Fetal Brain Male	brain
32	chr11:74039000-74053000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr11:74039200-74055200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:74039400-74071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:74039600-74052200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr11:74039800-74066200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr11:74040800-74049800	Weak transcription	Thymus	Thymus
38	chr11:74040800-74051400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr11:74041600-74049800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr11:74041600-74052800	Weak transcription	Fetal Lung	lung
41	chr11:74041800-74071200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:74041800-74071400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:74042000-74051000	Weak transcription	HMEC	breast
44	chr11:74042000-74077600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr11:74042200-74065600	Weak transcription	Fetal Heart	heart
46	chr11:74042200-74081200	Weak transcription	Hela-S3	cervix
47	chr11:74042400-74053200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr11:74042800-74050400	Weak transcription	Pancreas	Pancrea
49	chr11:74043200-74054000	Weak transcription	Right Ventricle	heart
50	chr11:74043400-74050200	Weak transcription	Fetal Intestine Small	intestine

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