Variant report

Variant	rs1389371
Chromosome Location	chr1:212410155-212410156
allele	C/T
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	RCOR1	chr1:212410068-212410314	K562	blood:	n/a	n/a
2	RCOR1	chr1:212410138-212410340	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212408314..212411280-chr1:212781747..212784026,2	K562	blood:

Variant related genes	Relation type
ENSG00000226251	TF binding region
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10019	0.96[CEU][hapmap]
rs1009622	0.83[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs11119884	0.84[JPT][hapmap]
rs11119885	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs11119887	0.83[ASN][1000 genomes]
rs11119904	0.83[EUR][1000 genomes]
rs12033246	0.96[CEU][hapmap]
rs12035647	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs12036130	0.86[EUR][1000 genomes]
rs12402397	0.83[CHB][hapmap]
rs1389369	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs1472226	0.83[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap]
rs17042034	0.83[EUR][1000 genomes]
rs1774249	0.92[CEU][hapmap]
rs1992643	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2001234	0.81[ASN][1000 genomes]
rs2012917	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs2087946	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs2252044	0.96[CEU][hapmap];0.86[TSI][hapmap]
rs2516331	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2589474	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099112	0.96[CEU][hapmap]
rs351373	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs351377	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs351378	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs351379	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs351380	0.82[EUR][1000 genomes]
rs351386	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs351393	0.96[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs351398	0.81[EUR][1000 genomes]
rs351401	0.83[EUR][1000 genomes]
rs351407	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs351408	0.96[CEU][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs351417	0.86[EUR][1000 genomes]
rs351419	0.89[EUR][1000 genomes]
rs3767861	0.96[CEU][hapmap];0.86[TSI][hapmap]
rs3767862	0.96[CEU][hapmap];0.86[TSI][hapmap]
rs4362041	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs4951582	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4951589	0.96[CEU][hapmap]
rs6540731	0.82[CHD][hapmap]
rs6540732	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs6540733	0.83[CHB][hapmap]
rs6657900	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs6668866	0.86[CHD][hapmap];0.89[JPT][hapmap]
rs6679796	0.89[JPT][hapmap]
rs7415843	0.96[CEU][hapmap]
rs7519168	0.86[CHD][hapmap];0.84[JPT][hapmap]
rs7519959	0.96[CEU][hapmap];0.86[TSI][hapmap]
rs7544225	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs867584	0.80[ASN][1000 genomes]
rs903121	0.83[CHB][hapmap];0.89[JPT][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1389371	TMEM206	cis	cerebellum	SCAN
rs1389371	SYT14	cis	cerebellum	SCAN
rs1389371	SLC30A1	cis	cerebellum	SCAN
rs1389371	CD34	cis	cerebellum	SCAN
rs1389371	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs1389371	TMEM206	cis	Esophagus Mucosa	GTEx
rs1389371	LGTN	cis	cerebellum	SCAN
rs1389371	TMEM206	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212404800-212410800	Enhancers	Skeletal Muscle Male	skeletal muscle
2	chr1:212405200-212410600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr1:212405600-212414800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:212405600-212416400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:212406400-212411000	Enhancers	HSMMtube	muscle
6	chr1:212406600-212410800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:212406800-212410400	Enhancers	HSMM	muscle
8	chr1:212406800-212410600	Enhancers	Stomach Mucosa	stomach
9	chr1:212407200-212410400	Enhancers	Left Ventricle	heart
10	chr1:212407600-212412400	Enhancers	Duodenum Mucosa	Duodenum
11	chr1:212407800-212410400	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr1:212407800-212412800	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr1:212408000-212410600	Enhancers	Fetal Heart	heart
14	chr1:212408000-212411600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:212408000-212411800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:212408000-212413000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr1:212408200-212415400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:212408400-212410200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:212408400-212411600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:212408400-212415600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:212408600-212410200	Weak transcription	HepG2	liver
22	chr1:212408600-212410400	Weak transcription	HMEC	breast
23	chr1:212408600-212410800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:212408600-212410800	Weak transcription	GM12878-XiMat	blood
25	chr1:212408600-212411000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:212408600-212411000	Weak transcription	NHDF-Ad	bronchial
27	chr1:212408600-212411200	Weak transcription	A549	lung
28	chr1:212408600-212411600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:212408600-212411600	Weak transcription	Adipose Nuclei	Adipose
30	chr1:212408600-212411600	Weak transcription	Brain Anterior Caudate	brain
31	chr1:212408600-212411600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:212408600-212411600	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:212408600-212411600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:212408600-212411600	Weak transcription	Spleen	Spleen
35	chr1:212408600-212411600	Weak transcription	HUVEC	blood vessel
36	chr1:212408600-212411800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:212408600-212411800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:212408600-212412000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:212408600-212414800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:212408600-212415000	Enhancers	K562	blood
41	chr1:212408600-212416000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:212408600-212416200	Weak transcription	Fetal Stomach	stomach
43	chr1:212408800-212411200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:212408800-212411600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:212408800-212411600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:212408800-212411600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr1:212409000-212411800	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr1:212409000-212413000	Enhancers	Fetal Intestine Small	intestine
49	chr1:212409000-212413000	Enhancers	Gastric	stomach
50	chr1:212409000-212413200	Enhancers	Fetal Intestine Large	intestine

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