Variant report

Variant	rs701905
Chromosome Location	chr1:212553111-212553112
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	chr1:212550848..212553114-chr1:212586010..212588532,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000065600	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10019	0.86[YRI][hapmap];0.82[EUR][1000 genomes]
rs1086893	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12023488	0.80[EUR][1000 genomes]
rs12033246	0.81[EUR][1000 genomes]
rs12035647	0.84[YRI][hapmap]
rs1539206	0.81[YRI][hapmap]
rs2252044	1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs3099112	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs351393	1.00[YRI][hapmap]
rs3767861	0.86[YRI][hapmap];0.82[EUR][1000 genomes]
rs3767862	0.86[YRI][hapmap];0.82[EUR][1000 genomes]
rs3767863	0.82[EUR][1000 genomes]
rs4951589	0.80[YRI][hapmap];0.81[EUR][1000 genomes]
rs518793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs612414	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6659594	0.82[EUR][1000 genomes]
rs7415843	1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs7519959	0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs792445	0.84[EUR][1000 genomes]
rs792447	1.00[YRI][hapmap]
rs792448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][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	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS 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 target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs701905	NENF	cis	Esophagus Mucosa	GTEx
rs701905	TMEM206	cis	Esophagus Mucosa	GTEx
rs701905	C1orf75	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212489600-212554800	Weak transcription	Small Intestine	intestine
2	chr1:212502600-212563400	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr1:212502600-212564600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr1:212524400-212554600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:212526800-212582800	Weak transcription	Fetal Brain Male	brain
6	chr1:212528400-212583000	Weak transcription	Fetal Kidney	kidney
7	chr1:212529400-212562400	Strong transcription	Dnd41	blood
8	chr1:212529800-212563200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:212532400-212560200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr1:212533400-212557000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:212534000-212558200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:212534000-212570200	Weak transcription	HSMM	muscle
13	chr1:212534400-212570600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:212534600-212560000	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:212535000-212561400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:212535200-212560200	Weak transcription	Hela-S3	cervix
17	chr1:212536200-212561600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:212538000-212571000	Weak transcription	NH-A	brain
19	chr1:212538200-212559600	Weak transcription	Right Atrium	heart
20	chr1:212540400-212575400	Weak transcription	HUVEC	blood vessel
21	chr1:212540600-212562600	Weak transcription	Osteobl	bone
22	chr1:212540600-212564000	Weak transcription	Stomach Mucosa	stomach
23	chr1:212540800-212556800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:212542800-212561600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:212543600-212565200	Weak transcription	Fetal Lung	lung
26	chr1:212545000-212561000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:212546600-212553800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:212546800-212554400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:212546800-212560200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:212546800-212560400	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:212547000-212553200	Strong transcription	K562	blood
32	chr1:212547000-212553400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:212547000-212553600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:212547000-212553600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:212547000-212553800	Strong transcription	Primary hematopoietic stem cells	blood
36	chr1:212547000-212562600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:212547000-212563400	Strong transcription	Fetal Thymus	thymus
38	chr1:212547200-212561000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:212547400-212562400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:212547400-212562400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:212548200-212560600	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr1:212548400-212553600	Strong transcription	Primary B cells from cord blood	blood
43	chr1:212548600-212553400	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr1:212548600-212553600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:212548600-212553800	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr1:212548600-212563800	Strong transcription	Primary T cells from cord blood	blood
47	chr1:212548800-212553800	Strong transcription	Thymus	Thymus
48	chr1:212548800-212558800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:212549000-212553600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:212549200-212553400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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