Variant report

Variant	rs6657065
Chromosome Location	chr1:67384639-67384640
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10749766	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789219	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889651	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1118392	0.90[EUR][1000 genomes]
rs11208971	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208973	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208974	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1121824	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12562761	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12742428	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535365	0.84[EUR][1000 genomes]
rs1570838	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925409	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1925410	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2065002	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755241	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755242	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755243	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755251	0.84[EUR][1000 genomes]
rs2755253	0.80[ASN][1000 genomes]
rs2755254	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755266	0.87[EUR][1000 genomes]
rs2755270	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755271	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2815349	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2815355	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2815360	0.84[EUR][1000 genomes]
rs2815362	0.84[EUR][1000 genomes]
rs2815363	0.84[EUR][1000 genomes]
rs2815364	0.84[EUR][1000 genomes]
rs2815365	0.84[EUR][1000 genomes]
rs2815366	0.84[EUR][1000 genomes]
rs2815367	0.84[EUR][1000 genomes]
rs2815368	0.83[EUR][1000 genomes]
rs2815374	0.82[AMR][1000 genomes]
rs3736905	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3929738	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4486425	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4570393	0.86[EUR][1000 genomes]
rs4581250	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4582760	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4655660	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655661	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655662	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv871720	chr1:67357596-67435161	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv947266	chr1:67358868-67399427	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv3448405	chr1:67360980-67393830	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6657065	SLC35D1	Cis_1M	lymphoblastoid	RTeQTL
rs6657065	MIER1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67348400-67389000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:67349400-67389600	Weak transcription	Aorta	Aorta
3	chr1:67352800-67385600	Weak transcription	Ovary	ovary
4	chr1:67359400-67389600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:67364000-67385800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:67364000-67389000	Weak transcription	Osteobl	bone
7	chr1:67364800-67388800	Weak transcription	NHDF-Ad	bronchial
8	chr1:67366600-67389000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:67367800-67385400	Weak transcription	Fetal Stomach	stomach
10	chr1:67369600-67385600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:67377200-67384800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:67377200-67389200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:67379200-67388600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:67380000-67388800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:67380400-67387600	Weak transcription	HepG2	liver
16	chr1:67382000-67385400	Enhancers	Fetal Intestine Small	intestine
17	chr1:67382200-67388800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:67382200-67389000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:67382200-67389200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:67382400-67385200	Weak transcription	Brain Germinal Matrix	brain
21	chr1:67382400-67385600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:67382400-67389200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:67382600-67385400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:67382600-67388800	Weak transcription	Brain Anterior Caudate	brain
25	chr1:67382800-67385800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:67383000-67385600	Weak transcription	Primary B cells from cord blood	blood
27	chr1:67383000-67389000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:67383200-67388000	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr1:67383200-67388800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:67383400-67387600	Weak transcription	K562	blood
31	chr1:67383400-67388800	Weak transcription	Fetal Brain Male	brain
32	chr1:67383400-67389200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:67383600-67386200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:67383600-67387800	Weak transcription	Primary T cells from cord blood	blood
35	chr1:67383800-67384800	Weak transcription	Fetal Intestine Large	intestine
36	chr1:67383800-67388200	Weak transcription	Fetal Heart	heart
37	chr1:67383800-67389000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:67384000-67389000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:67384200-67384800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:67384200-67386400	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr1:67384400-67388800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:67384400-67389200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr1:67384400-67389600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:67384600-67385600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:67384600-67388600	Weak transcription	Brain Angular Gyrus	brain
46	chr1:67384600-67388800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:67384600-67389000	Weak transcription	Duodenum Mucosa	Duodenum

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