Variant report

Variant	rs11694383
Chromosome Location	chr2:39012856-39012857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:38974982..38979904-chr2:39002191..39014206,31	MCF-7	breast:
2	chr2:38976960..38980095-chr2:39010307..39015604,4	K562	blood:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10173118	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10173240	0.94[CHB][hapmap];0.91[EUR][1000 genomes]
rs10176932	0.94[CHB][hapmap]
rs10197412	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10865143	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10865144	0.90[EUR][1000 genomes]
rs11124646	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs11889280	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12465043	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12468732	0.83[ASN][1000 genomes]
rs12469681	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12472454	0.81[EUR][1000 genomes]
rs12473036	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12477252	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12618118	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12712621	0.87[CHB][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12712622	0.82[EUR][1000 genomes]
rs12991609	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12996194	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13011522	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13014136	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13029406	0.94[CHB][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13383541	0.94[CHB][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13411868	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13417196	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1530852	0.94[CHB][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1530853	0.94[CHB][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1979142	0.94[CHB][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1997377	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs2037875	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2272445	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs2373473	0.90[JPT][hapmap]
rs3099940	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs3099941	0.90[JPT][hapmap]
rs3099943	1.00[JPT][hapmap]
rs3099945	1.00[JPT][hapmap]
rs3099952	1.00[ASN][1000 genomes]
rs3099960	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3099965	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3099984	0.81[EUR][1000 genomes]
rs3099985	0.83[EUR][1000 genomes]
rs3099987	0.83[EUR][1000 genomes]
rs3099988	0.82[EUR][1000 genomes]
rs3099989	0.82[EUR][1000 genomes]
rs3099991	0.84[EUR][1000 genomes]
rs3112140	0.90[EUR][1000 genomes]
rs3112149	0.81[EUR][1000 genomes]
rs3112198	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3112200	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112205	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112209	0.92[ASN][1000 genomes]
rs3112210	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3112215	0.88[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs3112216	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3770681	0.94[CHB][hapmap]
rs4602206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4630748	0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4670894	0.86[ASN][1000 genomes]
rs4670897	0.91[EUR][1000 genomes]
rs56393601	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60012208	0.83[EUR][1000 genomes]
rs62144837	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6544175	0.95[ASN][1000 genomes]
rs6715866	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6728394	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs6753251	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6756847	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs7419616	0.94[CHB][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7419838	0.94[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7588621	0.80[EUR][1000 genomes]
rs7589162	0.94[CHB][hapmap];0.84[EUR][1000 genomes]
rs7602287	0.81[EUR][1000 genomes]
rs7603676	0.94[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats 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 target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
4	nsv1014616	chr2:38985472-39022893	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11694383	SFRS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39005800-39037400	Weak transcription	Esophagus	oesophagus
2	chr2:39006000-39016000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:39006000-39037600	Weak transcription	Aorta	Aorta
4	chr2:39006000-39037600	Weak transcription	Gastric	stomach
5	chr2:39006200-39025200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:39006200-39029200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:39006200-39029800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:39006200-39031800	Weak transcription	Right Ventricle	heart
9	chr2:39006400-39018800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:39006400-39024000	Weak transcription	Osteobl	bone
11	chr2:39006400-39025200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:39006400-39025200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:39006400-39029600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:39006400-39037800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr2:39006400-39045600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:39006600-39025200	Weak transcription	Fetal Brain Female	brain
18	chr2:39006600-39031600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:39006600-39032200	Weak transcription	Colon Smooth Muscle	Colon
20	chr2:39006600-39033600	Weak transcription	GM12878-XiMat	blood
21	chr2:39006600-39038200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:39006800-39031800	Weak transcription	Fetal Brain Male	brain
23	chr2:39008800-39024200	Weak transcription	Left Ventricle	heart
24	chr2:39009000-39024600	Weak transcription	Spleen	Spleen
25	chr2:39009000-39024600	Weak transcription	Dnd41	blood
26	chr2:39009000-39027400	Weak transcription	Thymus	Thymus
27	chr2:39009000-39027800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:39009000-39029200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:39009000-39037400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:39009200-39015400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:39009200-39018600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr2:39009200-39018600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr2:39009200-39024000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:39009200-39024200	Weak transcription	Brain Anterior Caudate	brain
35	chr2:39009200-39024400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:39009200-39024400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:39009200-39024400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:39009200-39024600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:39009200-39024600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:39009200-39024600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:39009200-39025000	Weak transcription	HSMM	muscle
42	chr2:39009200-39027600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:39009200-39027800	Weak transcription	Brain Substantia Nigra	brain
44	chr2:39009200-39029600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:39009200-39029800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr2:39009200-39032000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:39009200-39032000	Weak transcription	K562	blood
48	chr2:39009200-39032400	Weak transcription	Primary B cells from cord blood	blood
49	chr2:39009200-39032400	Weak transcription	Brain Angular Gyrus	brain
50	chr2:39009200-39037600	Weak transcription	H1 Cell Line	embryonic stem cell

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