Variant report

Variant	rs2985711
Chromosome Location	chr1:156282224-156282225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:156279316..156282501-chr1:156303484..156305928,3	MCF-7	breast:
2	chr1:156281694..156285045-chr1:156287346..156289358,3	MCF-7	breast:
3	chr1:156250357..156252428-chr1:156281339..156284040,2	MCF-7	breast:
4	chr1:156252777..156254297-chr1:156281743..156283366,2	MCF-7	breast:
5	chr1:156235066..156236811-chr1:156280400..156283340,2	K562	blood:
6	chr1:156281112..156282733-chr1:156283944..156286193,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163472	Chromatin interaction
ENSG00000163468	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2246476	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2253358	0.94[CEU][hapmap];0.90[CHB][hapmap]
rs2495269	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2540168	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs2540169	0.82[CEU][hapmap];0.85[CHB][hapmap]
rs2764406	0.94[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2764407	0.94[CEU][hapmap];0.85[CHB][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases
2	nsv1011302	chr1:156081561-156532624	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	380 gene(s)	inside rSNPs	diseases
3	nsv915822	chr1:156226286-156651655	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	367 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2985711	SMG5	cis	Whole Blood	GTEx
rs2985711	PAQR6	cis	Whole Blood	GTEx
rs2985711	C1orf85	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:156265800-156286200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:156271800-156290000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:156272400-156297200	Strong transcription	Fetal Stomach	stomach
4	chr1:156272600-156297000	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:156272800-156283200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:156272800-156297000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:156272800-156297000	Strong transcription	Liver	Liver
8	chr1:156273000-156297200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:156273000-156297200	Strong transcription	Fetal Muscle Leg	muscle
10	chr1:156273000-156306200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:156273200-156296200	Strong transcription	Fetal Muscle Trunk	muscle
12	chr1:156273600-156297200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:156273600-156297200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:156273800-156296800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:156273800-156296800	Strong transcription	Placenta	Placenta
16	chr1:156273800-156296800	Strong transcription	Fetal Thymus	thymus
17	chr1:156273800-156297200	Strong transcription	Fetal Intestine Small	intestine
18	chr1:156274000-156297200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:156274000-156305600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:156274200-156283800	Strong transcription	Fetal Brain Female	brain
21	chr1:156274200-156293000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:156274200-156295200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:156274200-156297200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:156274400-156296200	Strong transcription	Thymus	Thymus
25	chr1:156274400-156297200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:156274400-156297800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:156274600-156296400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:156274600-156305800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:156275000-156297200	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr1:156275000-156297200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:156275000-156297200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:156275200-156295400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:156275200-156296200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:156275200-156297000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:156275800-156296200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr1:156276200-156296000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr1:156276400-156283600	Strong transcription	Right Ventricle	heart
38	chr1:156276400-156291000	Strong transcription	Small Intestine	intestine
39	chr1:156276400-156296000	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:156276400-156296800	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:156276400-156297200	Strong transcription	Dnd41	blood
42	chr1:156276800-156295200	Strong transcription	Lung	lung
43	chr1:156277000-156282600	Strong transcription	Psoas Muscle	Psoas
44	chr1:156277000-156290600	Strong transcription	Hela-S3	cervix
45	chr1:156277000-156295000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr1:156277000-156295200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:156277000-156295200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:156277000-156295200	Strong transcription	Brain Hippocampus Middle	brain
49	chr1:156277000-156296000	Strong transcription	Brain Cingulate Gyrus	brain
50	chr1:156277000-156296000	Strong transcription	Fetal Intestine Large	intestine

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