Variant report

Variant	rs1143
Chromosome Location	chr7:104756344-104756345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:104744452..104748663-chr7:104752143..104756800,5	K562	blood:
2	chr7:104748748..104753813-chr7:104754456..104758355,8	K562	blood:

Variant related genes	Relation type
ENSG00000005483	Chromatin interaction
ENSG00000272918	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1013016	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.99[ASN][1000 genomes]
rs1019040	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.99[ASN][1000 genomes]
rs10224526	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[ASN][1000 genomes]
rs10231975	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10241374	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10242713	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs10244764	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs10245589	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[ASN][1000 genomes]
rs10245676	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs10245796	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10248422	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10248954	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10252295	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10253962	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10260346	0.91[ASN][1000 genomes]
rs10261472	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10261573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10264273	0.83[ASN][1000 genomes]
rs10268866	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[ASN][1000 genomes]
rs10269027	0.81[CHB][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap]
rs10276583	0.86[CHB][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap]
rs10279486	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10280470	0.81[CHB][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap]
rs10280752	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[ASN][1000 genomes]
rs10808139	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[ASN][1000 genomes]
rs10808140	0.81[CHB][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap]
rs10953464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10953467	0.95[ASN][1000 genomes]
rs10953473	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1142	0.82[ASN][1000 genomes]
rs11973516	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs11976329	0.96[ASN][1000 genomes]
rs11981399	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12531424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12532062	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12532456	0.94[ASN][1000 genomes]
rs12534140	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs12540007	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12671368	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs12705297	0.90[ASN][1000 genomes]
rs12705299	0.90[ASN][1000 genomes]
rs12705305	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs13237370	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17721991	0.89[JPT][hapmap]
rs1859786	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1967301	0.96[ASN][1000 genomes]
rs1978201	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2003506	0.81[ASN][1000 genomes]
rs2058711	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2214928	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.96[ASN][1000 genomes]
rs2216107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2237602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2237605	0.93[ASN][1000 genomes]
rs2237606	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2237608	0.96[ASN][1000 genomes]
rs2237610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2237615	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2237616	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2237617	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs2237618	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2237619	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2237620	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2240453	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs2240454	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[ASN][1000 genomes]
rs2240455	0.81[CHB][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap]
rs2240457	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs2240465	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2283016	0.93[ASN][1000 genomes]
rs2299297	0.96[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2299299	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2299313	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2299320	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2299326	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2385542	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs28489493	0.94[ASN][1000 genomes]
rs3173872	0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap]
rs3213676	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs34202980	0.89[ASN][1000 genomes]
rs35418021	0.94[ASN][1000 genomes]
rs3779208	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs3801283	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs3815256	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs4730067	0.89[JPT][hapmap];0.85[MEX][hapmap]
rs4730068	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs4730069	0.91[ASN][1000 genomes]
rs4730071	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs6466043	0.96[ASN][1000 genomes]
rs6466044	0.93[ASN][1000 genomes]
rs6466045	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs6466046	0.96[ASN][1000 genomes]
rs67739707	0.81[ASN][1000 genomes]
rs6952534	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6971241	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs6973052	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs717352	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs725506	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs740297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs740298	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs740300	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs7780887	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs7783812	0.95[ASN][1000 genomes]
rs7785197	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs7787448	0.95[ASN][1000 genomes]
rs7787558	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7805792	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7808168	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7810119	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8180737	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs875568	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs960437	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs9641340	0.94[ASN][1000 genomes]
rs9641343	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs9641345	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs999895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv888927	chr7:104614664-104781644	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv608068	chr7:104622402-104757483	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
3	esv34588	chr7:104737612-105153242	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1143	LRWD1	cis	parietal	SCAN
rs1143	ATXN7L1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104677800-104758200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:104678000-104812200	Strong transcription	Dnd41	blood
3	chr7:104681200-104758400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:104681200-104760400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr7:104685600-104759000	Strong transcription	Primary B cells from peripheral blood	blood
6	chr7:104701400-104758800	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr7:104702800-104758800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:104703600-104759000	Strong transcription	Fetal Intestine Large	intestine
9	chr7:104706000-104760200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:104712400-104758800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr7:104722200-104759400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr7:104727800-104758200	Strong transcription	Fetal Thymus	thymus
13	chr7:104727800-104759200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:104727800-104759800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr7:104727800-104760400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr7:104728000-104760200	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr7:104728200-104758400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr7:104728200-104758400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr7:104728400-104756800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:104728400-104758400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr7:104728400-104758400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:104737000-104757800	Strong transcription	Adipose Nuclei	Adipose
23	chr7:104737800-104758800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr7:104738600-104758400	Strong transcription	Fetal Lung	lung
25	chr7:104738800-104760200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:104739000-104759200	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr7:104739800-104757800	Strong transcription	HSMM	muscle
28	chr7:104740000-104758400	Strong transcription	NHDF-Ad	bronchial
29	chr7:104740200-104759000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr7:104740200-104759400	Strong transcription	Primary B cells from cord blood	blood
31	chr7:104740400-104758200	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr7:104740400-104759200	Strong transcription	Primary T cells from cord blood	blood
33	chr7:104740400-104787400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:104740800-104756800	Strong transcription	K562	blood
35	chr7:104740800-104758400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr7:104740800-104760200	Strong transcription	HMEC	breast
37	chr7:104741400-104757800	Strong transcription	HUVEC	blood vessel
38	chr7:104741600-104758600	Strong transcription	Placenta	Placenta
39	chr7:104741800-104756400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:104742200-104759800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr7:104742400-104760200	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr7:104742800-104758400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr7:104743200-104756400	Strong transcription	A549	lung
44	chr7:104743600-104757400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:104743800-104756800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr7:104743800-104758600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr7:104743800-104758600	Strong transcription	GM12878-XiMat	blood
48	chr7:104745200-104758600	Strong transcription	Primary hematopoietic stem cells	blood
49	chr7:104746000-104756400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr7:104750200-104777000	Weak transcription	Right Atrium	heart

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