Variant report

Variant	rs701907
Chromosome Location	chr1:212521404-212521405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212514803..212516600-chr1:212518695..212521669,2	MCF-7	breast:
2	chr1:212519088..212521774-chr1:212528493..212530419,2	MCF-7	breast:
3	chr1:212515457..212517203-chr1:212520374..212522955,2	K562	blood:
4	chr1:212518997..212521447-chr1:212525438..212527861,2	K562	blood:

Variant related genes	Relation type
ENSG00000201544	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1086892	1.00[ASW][hapmap];0.91[LWK][hapmap]
rs12725070	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1444692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1774252	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2921127	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2921128	0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2921129	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2995255	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2995256	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2995257	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2995258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099111	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121291	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs351383	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs351392	0.86[GIH][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs351395	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs351397	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs351405	0.80[EUR][1000 genomes]
rs351413	0.81[GIH][hapmap]
rs351416	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs351420	0.81[EUR][1000 genomes]
rs4554777	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951584	0.93[CEU][hapmap]
rs6674587	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs701906	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs701908	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs792433	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs792434	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs792440	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs792441	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs792442	1.00[ASW][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs792443	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs812074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs701907	IL24	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212467400-212526000	Weak transcription	A549	lung
2	chr1:212479200-212525400	Weak transcription	Aorta	Aorta
3	chr1:212486200-212526000	Weak transcription	HUVEC	blood vessel
4	chr1:212489600-212554800	Weak transcription	Small Intestine	intestine
5	chr1:212493800-212533400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:212498000-212526200	Weak transcription	Fetal Brain Male	brain
7	chr1:212499800-212525400	Weak transcription	Gastric	stomach
8	chr1:212500000-212540400	Weak transcription	Stomach Mucosa	stomach
9	chr1:212501000-212533600	Weak transcription	Fetal Heart	heart
10	chr1:212501400-212525800	Weak transcription	Pancreas	Pancrea
11	chr1:212501400-212526200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:212501400-212540800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:212501800-212540800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:212502200-212526000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:212502400-212528200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:212502600-212563400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr1:212502600-212564600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:212502800-212541400	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:212504000-212548600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:212504200-212525600	Weak transcription	Spleen	Spleen
21	chr1:212504400-212537600	Weak transcription	Psoas Muscle	Psoas
22	chr1:212504800-212525800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:212504800-212526000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:212505000-212525600	Weak transcription	Colonic Mucosa	Colon
25	chr1:212505200-212531400	Weak transcription	HMEC	breast
26	chr1:212505800-212533200	Weak transcription	NH-A	brain
27	chr1:212507400-212525400	Weak transcription	Esophagus	oesophagus
28	chr1:212507400-212525600	Weak transcription	Brain Anterior Caudate	brain
29	chr1:212507400-212526000	Weak transcription	HSMM	muscle
30	chr1:212507600-212526000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:212507800-212526000	Weak transcription	Fetal Brain Female	brain
32	chr1:212508000-212523400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:212508000-212525600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:212508000-212525800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:212508000-212525800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:212508000-212526000	Weak transcription	Brain Substantia Nigra	brain
37	chr1:212508200-212524800	Weak transcription	Lung	lung
38	chr1:212508200-212526000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:212508200-212526400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:212508200-212528000	Weak transcription	Fetal Kidney	kidney
41	chr1:212508200-212545800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:212508400-212525800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:212508600-212525600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:212508600-212541000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:212509000-212521600	Weak transcription	Hela-S3	cervix
46	chr1:212509000-212525600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:212509000-212525600	Weak transcription	NHEK	skin
48	chr1:212509600-212523400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr1:212511400-212540800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr1:212513200-212521800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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