Variant report

Variant	rs7641410
Chromosome Location	chr3:112959208-112959209
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10511323	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710894	0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs11717833	0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs11919134	0.82[MEX][hapmap]
rs11928342	0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12485329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492273	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[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];0.97[ASN][1000 genomes]
rs12494864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12631733	0.90[CHB][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs12638030	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16860758	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16860787	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1875111	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2036282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2201971	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34284771	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3814398	0.95[CHB][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs3846046	0.86[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3856718	0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3856719	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3856720	0.93[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682131	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4682478	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682479	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682480	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4682481	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682483	0.82[EUR][1000 genomes]
rs55814436	0.86[AMR][1000 genomes]
rs73235136	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73235142	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73235143	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73235147	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs775222	0.93[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7641410	BOC	cis	parietal	SCAN
rs7641410	CRYL1	trans	lymphoblastoid	seeQTL
rs7641410	CD96	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112932000-112972800	Weak transcription	Aorta	Aorta
2	chr3:112943600-112960600	Weak transcription	Fetal Thymus	thymus
3	chr3:112951200-112967000	Weak transcription	Colonic Mucosa	Colon
4	chr3:112951600-112960200	Weak transcription	NHLF	lung
5	chr3:112953000-112959800	Weak transcription	Fetal Brain Female	brain
6	chr3:112953800-112959600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:112953800-112959600	Weak transcription	Esophagus	oesophagus
8	chr3:112953800-112959600	Weak transcription	Fetal Brain Male	brain
9	chr3:112953800-112960600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:112953800-112965600	Weak transcription	Right Atrium	heart
11	chr3:112954000-112959600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr3:112954200-112959600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:112954200-112959600	Weak transcription	Osteobl	bone
14	chr3:112954200-112960400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:112954200-112965600	Weak transcription	Brain Substantia Nigra	brain
16	chr3:112954400-112959600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:112954400-112959600	Weak transcription	Fetal Lung	lung
18	chr3:112954400-112960200	Weak transcription	HSMM	muscle
19	chr3:112954600-112959600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:112954600-112959600	Weak transcription	NHEK	skin
21	chr3:112954600-112959800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:112954600-112960400	Weak transcription	HSMMtube	muscle
23	chr3:112957200-112959800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:112957600-112960800	Enhancers	Ovary	ovary
25	chr3:112957800-112961800	Enhancers	Rectal Smooth Muscle	rectum
26	chr3:112958200-112959800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:112958200-112960200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:112958400-112959400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
29	chr3:112958400-112959600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:112958400-112960000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:112958400-112960200	Enhancers	NHDF-Ad	bronchial
32	chr3:112958400-112960600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:112958400-112960800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:112958400-112960800	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr3:112958400-112963000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:112958600-112959800	Enhancers	Placenta	Placenta
37	chr3:112958600-112960000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:112958600-112960800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:112958600-112961800	Enhancers	Colon Smooth Muscle	Colon
40	chr3:112958600-112962200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:112958600-112969000	Weak transcription	Spleen	Spleen
42	chr3:112958800-112959600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:112958800-112960200	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr3:112958800-112960400	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr3:112958800-112960400	Genic enhancers	Fetal Stomach	stomach
46	chr3:112958800-112960400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr3:112958800-112960800	Enhancers	Fetal Kidney	kidney
48	chr3:112958800-112961000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr3:112958800-112962200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:112958800-112962800	Enhancers	H1 Cell Line	embryonic stem cell

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