Variant report

Variant	rs6661806
Chromosome Location	chr1:10037468-10037469
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10036550..10039108-chr1:10039716..10041886,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173614	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10779734	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11121510	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11121512	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11828	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12140009	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12140015	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12140058	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1220389	0.86[ASN][1000 genomes]
rs1220397	0.83[ASN][1000 genomes]
rs1220398	0.87[CHB][hapmap]
rs1220399	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1220400	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1220402	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1220420	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1220421	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1220424	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1234694	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1628143	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1660733	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2890358	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2919694	0.85[ASN][1000 genomes]
rs3003376	0.84[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3003377	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3003378	0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3013783	0.85[ASN][1000 genomes]
rs3013784	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3013788	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3123522	0.85[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6541073	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6664631	0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6678023	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6680076	0.87[ASN][1000 genomes]
rs7517360	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7517806	0.86[ASN][1000 genomes]
rs7517812	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7539191	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription 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	549 gene(s)	inside rSNPs	diseases
2	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
4	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv1005461	chr1:9972921-10038862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
9	nsv534855	chr1:9972921-10038862	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6661806	LZIC	cis	Lymphoblastoid	GTEx
rs6661806	LZIC	Cis_1M	lymphoblastoid	RTeQTL
rs6661806	LZIC	cis	multi-tissue	Pritchard

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10011000-10044800	Weak transcription	NHDF-Ad	bronchial
2	chr1:10011800-10042200	Weak transcription	K562	blood
3	chr1:10016400-10042400	Weak transcription	HMEC	breast
4	chr1:10019800-10037600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:10021400-10039200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:10021400-10043200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:10021600-10041600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:10021600-10041600	Weak transcription	HSMMtube	muscle
9	chr1:10021600-10049000	Weak transcription	HSMM	muscle
10	chr1:10021800-10037600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:10023400-10044000	Weak transcription	HepG2	liver
12	chr1:10025800-10046800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:10028400-10050000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:10029600-10041000	Weak transcription	Osteobl	bone
15	chr1:10029600-10042200	Weak transcription	GM12878-XiMat	blood
16	chr1:10030400-10041000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:10030400-10043000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:10030800-10044600	Weak transcription	Brain Germinal Matrix	brain
19	chr1:10031200-10042200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:10031200-10042200	Weak transcription	Small Intestine	intestine
21	chr1:10031600-10038400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:10031600-10039000	Strong transcription	Stomach Smooth Muscle	stomach
23	chr1:10031600-10039600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:10031600-10044600	Strong transcription	Fetal Intestine Large	intestine
25	chr1:10031600-10045600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:10031600-10046200	Strong transcription	Fetal Intestine Small	intestine
27	chr1:10031600-10047200	Strong transcription	Fetal Stomach	stomach
28	chr1:10031800-10039000	Strong transcription	Lung	lung
29	chr1:10031800-10039200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:10031800-10039600	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:10032000-10038000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:10032000-10038400	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr1:10032000-10039200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:10032000-10039400	Strong transcription	Duodenum Mucosa	Duodenum
35	chr1:10032000-10039600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr1:10032000-10039600	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:10032000-10039800	Strong transcription	Fetal Muscle Leg	muscle
38	chr1:10032000-10043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:10032000-10045200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr1:10032000-10046600	Strong transcription	Liver	Liver
41	chr1:10032200-10038600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:10032200-10039000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:10032200-10039000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:10032200-10039400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:10032200-10039600	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:10032200-10044200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:10032200-10044200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:10032200-10045400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:10032400-10038000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:10032400-10039400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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