Variant report

Variant	rs1570838
Chromosome Location	chr1:67403315-67403316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:67396141..67398449-chr1:67400881..67403704,2	MCF-7	breast:
2	chr1:65634867..65636428-chr1:67400742..67403571,2	MCF-7	breast:
3	chr1:67402975..67406629-chr1:67416021..67418318,3	K562	blood:

Variant related genes	Relation type
ENSG00000198160	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10749766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889651	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1118392	0.92[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs11208971	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208973	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208974	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208979	0.90[JPT][hapmap]
rs1121824	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12041926	0.90[JPT][hapmap]
rs12044278	0.92[JPT][hapmap]
rs12131222	0.92[JPT][hapmap]
rs12137403	0.90[JPT][hapmap]
rs12562761	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12742428	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs17497828	0.90[JPT][hapmap]
rs1925408	0.90[JPT][hapmap]
rs1925409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1925410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1925411	0.92[JPT][hapmap]
rs1925413	0.92[JPT][hapmap]
rs2025608	0.92[JPT][hapmap]
rs2065000	0.92[JPT][hapmap]
rs2065001	0.90[JPT][hapmap]
rs2065002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2182143	0.90[JPT][hapmap]
rs2755241	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755243	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755244	0.90[JPT][hapmap]
rs2755245	0.90[JPT][hapmap]
rs2755246	0.90[JPT][hapmap]
rs2755250	0.92[JPT][hapmap]
rs2755251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2755253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2755254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755256	0.82[JPT][hapmap]
rs2755266	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2755270	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2755271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2815349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2815351	0.90[JPT][hapmap]
rs2815355	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2815359	0.90[JPT][hapmap]
rs2815360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2815361	0.90[JPT][hapmap]
rs2815362	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2815363	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2815364	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2815365	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2815366	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2815367	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2815368	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2815370	0.90[JPT][hapmap]
rs2815371	0.90[JPT][hapmap]
rs2815374	0.84[AMR][1000 genomes]
rs2985795	0.92[JPT][hapmap]
rs2985797	0.90[JPT][hapmap]
rs2985818	0.90[JPT][hapmap]
rs2985821	0.92[JPT][hapmap]
rs2985822	0.90[JPT][hapmap]
rs2985824	0.90[JPT][hapmap]
rs2985825	0.90[JPT][hapmap]
rs2985826	0.92[JPT][hapmap]
rs3008848	0.90[JPT][hapmap]
rs3008853	0.92[JPT][hapmap]
rs3008854	0.92[JPT][hapmap]
rs3008855	0.90[JPT][hapmap]
rs3008858	0.92[JPT][hapmap]
rs3008871	0.81[JPT][hapmap]
rs3008892	0.90[JPT][hapmap]
rs3736905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3929738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4486425	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4570393	0.85[EUR][1000 genomes]
rs4581250	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4582760	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4620509	0.92[JPT][hapmap]
rs4655658	0.92[JPT][hapmap]
rs4655660	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4655663	0.90[JPT][hapmap]
rs6657065	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673462	0.92[JPT][hapmap]
rs912797	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1570838	MIER1	Cis_1M	lymphoblastoid	RTeQTL
rs1570838	SLC35D1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67396600-67416600	Weak transcription	Spleen	Spleen
2	chr1:67396800-67411200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:67396800-67414400	Weak transcription	Lung	lung
4	chr1:67396800-67429800	Weak transcription	Pancreas	Pancrea
5	chr1:67396800-67458200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:67396800-67459000	Weak transcription	Esophagus	oesophagus
7	chr1:67397000-67408000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:67397000-67409200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:67397600-67411000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:67397600-67411200	Weak transcription	Placenta	Placenta
11	chr1:67397600-67411200	Weak transcription	Fetal Stomach	stomach
12	chr1:67397600-67413000	Weak transcription	Fetal Brain Female	brain
13	chr1:67397600-67413000	Weak transcription	Fetal Kidney	kidney
14	chr1:67397600-67416600	Weak transcription	Right Ventricle	heart
15	chr1:67397600-67424400	Weak transcription	Colonic Mucosa	Colon
16	chr1:67397600-67457600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:67397800-67404200	Weak transcription	Fetal Intestine Large	intestine
18	chr1:67397800-67412400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:67397800-67412400	Weak transcription	Brain Germinal Matrix	brain
20	chr1:67398400-67412200	Weak transcription	Fetal Brain Male	brain
21	chr1:67398400-67414000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:67398600-67406400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:67398600-67411000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:67399000-67416400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:67399200-67406400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:67399600-67407400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:67399800-67409200	Weak transcription	Fetal Heart	heart
28	chr1:67399800-67411200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:67400000-67403600	Weak transcription	NH-A	brain
30	chr1:67400000-67403600	Weak transcription	NHDF-Ad	bronchial
31	chr1:67400000-67405200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:67400000-67408000	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:67400000-67411200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:67400200-67403600	Weak transcription	Primary B cells from cord blood	blood
35	chr1:67400200-67406200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:67400200-67410200	Weak transcription	HSMMtube	muscle
37	chr1:67400400-67403600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:67400400-67404000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:67400400-67404000	Weak transcription	HSMM	muscle
40	chr1:67400400-67404800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:67400400-67406400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr1:67400400-67409800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr1:67400400-67410600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:67400400-67413200	Weak transcription	Brain Substantia Nigra	brain
45	chr1:67400400-67413200	Weak transcription	Fetal Lung	lung
46	chr1:67400600-67403400	Weak transcription	NHLF	lung
47	chr1:67400600-67403600	Weak transcription	HUVEC	blood vessel
48	chr1:67400600-67405600	Weak transcription	Fetal Thymus	thymus
49	chr1:67400600-67406200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:67400600-67406400	Weak transcription	Primary hematopoietic stem cells	blood

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