Variant report

Variant	rs1009622
Chromosome Location	chr1:212412332-212412333
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:212412074-212412389	MCF-7	breast:	n/a	n/a
2	GATA3	chr1:212411939-212412443	T-47D	breast:	n/a	n/a
3	GATA3	chr1:212411895-212412468	T-47D	breast:	n/a	n/a
4	FOXA1	chr1:212412000-212412335	T-47D	breast:	n/a	n/a
5	MAFK	chr1:212412147-212412337	HepG2	liver:	n/a	chr1:212412211-212412226

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212412059..212414771-chr1:212457141..212460408,3	K562	blood:

Variant related genes	Relation type
ENSG00000226251	TF binding region
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11119884	0.91[CHB][hapmap]
rs11119885	0.83[CHB][hapmap]
rs11119887	0.85[ASN][1000 genomes]
rs12402397	0.83[CHB][hapmap]
rs1389369	0.83[CHB][hapmap]
rs1389371	0.83[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs1472226	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs2001234	0.81[ASN][1000 genomes]
rs2012917	0.83[CHB][hapmap]
rs2087946	0.83[CHB][hapmap]
rs2516331	0.96[ASN][1000 genomes]
rs2589474	0.94[ASN][1000 genomes]
rs351373	0.98[ASN][1000 genomes]
rs351377	0.99[ASN][1000 genomes]
rs351378	0.99[ASN][1000 genomes]
rs351379	0.99[ASN][1000 genomes]
rs351386	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs351407	0.94[ASN][1000 genomes]
rs351408	0.91[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs4362041	0.83[CHB][hapmap]
rs4951582	0.93[ASN][1000 genomes]
rs6540731	0.91[CHB][hapmap];0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs6540732	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs6540733	0.83[CHB][hapmap]
rs6540734	0.80[ASN][1000 genomes]
rs6657900	0.83[CHB][hapmap]
rs6668866	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs6679796	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs7511781	0.80[ASN][1000 genomes]
rs7515645	0.80[ASN][1000 genomes]
rs7519168	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs7544225	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs867584	0.80[ASN][1000 genomes]
rs903121	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1009622	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs1009622	PIGR	cis	cerebellum	SCAN
rs1009622	TMEM206	cis	parietal	SCAN
rs1009622	TMEM206	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212405600-212414800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:212405600-212416400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:212407600-212412400	Enhancers	Duodenum Mucosa	Duodenum
4	chr1:212407800-212412800	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr1:212408000-212413000	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr1:212408200-212415400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:212408400-212415600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:212408600-212414800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:212408600-212415000	Enhancers	K562	blood
10	chr1:212408600-212416000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:212408600-212416200	Weak transcription	Fetal Stomach	stomach
12	chr1:212409000-212413000	Enhancers	Fetal Intestine Small	intestine
13	chr1:212409000-212413000	Enhancers	Gastric	stomach
14	chr1:212409000-212413200	Enhancers	Fetal Intestine Large	intestine
15	chr1:212409400-212413000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:212409600-212412800	Enhancers	Liver	Liver
17	chr1:212410200-212417000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:212410600-212416200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr1:212410800-212412400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:212410800-212412400	Enhancers	NHEK	skin
21	chr1:212411000-212412400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:212411000-212412400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:212411400-212412400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:212411600-212412400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:212411600-212412400	Enhancers	Adipose Nuclei	Adipose
26	chr1:212411600-212412400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:212411600-212412400	Enhancers	Fetal Heart	heart
28	chr1:212411600-212412400	Enhancers	Fetal Lung	lung
29	chr1:212411600-212412400	Enhancers	Left Ventricle	heart
30	chr1:212411600-212412800	Enhancers	Lung	lung
31	chr1:212411600-212412800	Enhancers	Psoas Muscle	Psoas
32	chr1:212411600-212413000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:212411600-212413000	Enhancers	Colon Smooth Muscle	Colon
34	chr1:212411600-212413000	Enhancers	Esophagus	oesophagus
35	chr1:212411600-212413000	Enhancers	Pancreas	Pancrea
36	chr1:212411600-212413000	Enhancers	Right Atrium	heart
37	chr1:212411600-212413000	Enhancers	Stomach Smooth Muscle	stomach
38	chr1:212411600-212413000	Enhancers	Spleen	Spleen
39	chr1:212411600-212413200	Enhancers	Rectal Smooth Muscle	rectum
40	chr1:212411600-212413200	Enhancers	Stomach Mucosa	stomach
41	chr1:212411800-212412400	Enhancers	Fetal Muscle Leg	muscle
42	chr1:212411800-212413000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:212411800-212413200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:212411800-212415600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:212412000-212412400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr1:212412000-212414200	Weak transcription	HepG2	liver
47	chr1:212412000-212414600	Weak transcription	HUVEC	blood vessel
48	chr1:212412000-212415200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:212412000-212415400	Weak transcription	Brain Anterior Caudate	brain
50	chr1:212412000-212415600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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