Variant report

Variant	rs6753251
Chromosome Location	chr2:39007114-39007115
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38974982..38979904-chr2:39002191..39014206,31	MCF-7	breast:
2	chr2:38975156..38979928-chr2:39002986..39007194,11	MCF-7	breast:
3	chr2:38975148..38982473-chr2:39000165..39007764,21	K562	blood:
4	chr2:38976218..38980921-chr2:39003670..39007764,15	K562	blood:
5	chr2:38966114..38968421-chr2:39005419..39007550,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10173118	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10173240	0.90[EUR][1000 genomes]
rs10197412	0.82[EUR][1000 genomes]
rs10865143	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10865144	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11694383	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11889280	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12465043	0.90[EUR][1000 genomes]
rs12468732	0.80[ASN][1000 genomes]
rs12469681	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12472454	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12473036	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12477252	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12618118	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12712621	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12712622	0.82[EUR][1000 genomes]
rs12991609	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12996194	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13011522	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13014136	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13029406	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13383541	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13411868	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13417196	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1530852	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1530853	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1979142	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2037875	0.81[EUR][1000 genomes]
rs3099952	0.97[ASN][1000 genomes]
rs3099960	0.96[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3099965	0.88[AMR][1000 genomes];0.97[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	0.81[EUR][1000 genomes]
rs3099991	0.83[EUR][1000 genomes]
rs3112140	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3112149	0.80[EUR][1000 genomes]
rs3112198	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3112200	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112205	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112209	0.89[ASN][1000 genomes]
rs3112210	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3112215	0.93[ASN][1000 genomes]
rs3112216	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4602206	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4630748	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4670894	0.83[ASN][1000 genomes]
rs4670897	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56393601	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60012208	0.83[EUR][1000 genomes]
rs62144837	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6544175	0.92[ASN][1000 genomes]
rs6715866	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7419616	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7419838	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7589162	0.83[EUR][1000 genomes]
rs7602287	0.80[EUR][1000 genomes]

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
rs6753251	SFRS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39005800-39007800	Weak transcription	Lung	lung
2	chr2:39005800-39037400	Weak transcription	Esophagus	oesophagus
3	chr2:39006000-39007400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:39006000-39007400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:39006000-39007600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:39006000-39007600	Weak transcription	Left Ventricle	heart
7	chr2:39006000-39008200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:39006000-39008400	Weak transcription	Placenta	Placenta
9	chr2:39006000-39008600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:39006000-39011800	Weak transcription	Pancreas	Pancrea
11	chr2:39006000-39012400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:39006000-39016000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:39006000-39037600	Weak transcription	Aorta	Aorta
14	chr2:39006000-39037600	Weak transcription	Gastric	stomach
15	chr2:39006200-39007600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:39006200-39007800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:39006200-39007800	Weak transcription	Ovary	ovary
18	chr2:39006200-39007800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:39006200-39008600	Weak transcription	Brain Angular Gyrus	brain
20	chr2:39006200-39008600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:39006200-39008600	Weak transcription	HSMM	muscle
22	chr2:39006200-39008600	Weak transcription	NHDF-Ad	bronchial
23	chr2:39006200-39010600	Weak transcription	Stomach Mucosa	stomach
24	chr2:39006200-39025200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:39006200-39029200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:39006200-39029800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:39006200-39031800	Weak transcription	Right Ventricle	heart
28	chr2:39006400-39007400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:39006400-39007600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:39006400-39007600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:39006400-39007600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr2:39006400-39008200	Weak transcription	Adipose Nuclei	Adipose
33	chr2:39006400-39008200	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:39006400-39008200	Weak transcription	HMEC	breast
35	chr2:39006400-39008200	Weak transcription	K562	blood
36	chr2:39006400-39008200	Weak transcription	NHEK	skin
37	chr2:39006400-39008400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:39006400-39008400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:39006400-39008400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:39006400-39008400	Weak transcription	Brain Anterior Caudate	brain
41	chr2:39006400-39008400	Weak transcription	Brain Substantia Nigra	brain
42	chr2:39006400-39008400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:39006400-39008400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr2:39006400-39008400	Weak transcription	HSMMtube	muscle
45	chr2:39006400-39008400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr2:39006400-39008400	Weak transcription	NHLF	lung
47	chr2:39006400-39008600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr2:39006400-39008600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:39006400-39008600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:39006400-39008600	Weak transcription	Primary monocytes fromperipheralblood	blood

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