Variant report

Variant	rs11724119
Chromosome Location	chr4:129768342-129768343
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129764059..129767011-chr4:129767338..129770023,2	MCF-7	breast:
2	chr4:129766486..129769711-chr4:129773177..129777072,3	K562	blood:
3	chr4:129760081..129763027-chr4:129766274..129768354,2	K562	blood:
4	chr4:129760081..129764752-chr4:129766854..129770363,4	K562	blood:
5	chr4:129736742..129738918-chr4:129767515..129769516,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10017436	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10032000	0.81[JPT][hapmap]
rs11098987	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731189	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs13143771	0.87[JPT][hapmap]
rs1425618	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1648062	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1668289	0.80[JPT][hapmap]
rs167618	0.94[ASW][hapmap];0.87[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17013778	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2016294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2162126	0.81[JPT][hapmap]
rs2217023	0.87[JPT][hapmap]
rs318502	0.81[JPT][hapmap]
rs318504	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs318505	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs318536	0.81[JPT][hapmap]
rs318543	0.81[JPT][hapmap]
rs318552	0.80[JPT][hapmap]
rs318555	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs318556	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4052	0.82[EUR][1000 genomes]
rs4975263	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975264	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4975266	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975268	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975274	0.81[JPT][hapmap]
rs55829553	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62317868	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6833391	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6844446	0.89[EUR][1000 genomes];0.87[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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv517249	chr4:129738328-129927804	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11724119	SCLT1	cis	cerebellum	SCAN
rs11724119	C4orf29	cis	cerebellum	SCAN
rs11724119	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs11724119	C4orf33	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129746800-129770200	Weak transcription	HMEC	breast
2	chr4:129753600-129798600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:129753800-129770400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:129753800-129795000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:129754400-129770600	Weak transcription	Fetal Kidney	kidney
6	chr4:129757000-129770000	Weak transcription	Small Intestine	intestine
7	chr4:129760400-129783400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:129761600-129769000	Enhancers	Right Atrium	heart
9	chr4:129761600-129770800	Strong transcription	NHDF-Ad	bronchial
10	chr4:129761600-129779400	Strong transcription	Fetal Stomach	stomach
11	chr4:129761600-129782000	Strong transcription	Fetal Intestine Small	intestine
12	chr4:129761600-129785000	Strong transcription	Thymus	Thymus
13	chr4:129761800-129775000	Strong transcription	GM12878-XiMat	blood
14	chr4:129762000-129782800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr4:129762200-129773800	Strong transcription	Dnd41	blood
16	chr4:129762200-129775000	Strong transcription	Fetal Thymus	thymus
17	chr4:129762400-129771800	Strong transcription	K562	blood
18	chr4:129762400-129775000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:129762400-129775000	Strong transcription	HSMM	muscle
20	chr4:129762400-129784200	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr4:129762600-129775000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr4:129762600-129775400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:129762800-129784200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:129763000-129768600	Weak transcription	Fetal Heart	heart
25	chr4:129763000-129774600	Strong transcription	Primary T cells from cord blood	blood
26	chr4:129763000-129783800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:129763000-129785800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:129763000-129787200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr4:129763200-129784000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
30	chr4:129763200-129784000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr4:129763400-129774800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:129763400-129784200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:129763600-129774600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr4:129763600-129774800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr4:129763600-129774800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:129763600-129774800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:129763600-129777400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:129763600-129780400	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr4:129763600-129786600	Strong transcription	Fetal Intestine Large	intestine
40	chr4:129763800-129768800	Genic enhancers	Left Ventricle	heart
41	chr4:129763800-129769200	Genic enhancers	Pancreas	Pancrea
42	chr4:129763800-129769600	Strong transcription	NH-A	brain
43	chr4:129763800-129774000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:129763800-129774400	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr4:129763800-129775000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:129763800-129775200	Strong transcription	Primary hematopoietic stem cells	blood
47	chr4:129763800-129776400	Strong transcription	Hela-S3	cervix
48	chr4:129763800-129776600	Strong transcription	Fetal Muscle Trunk	muscle
49	chr4:129763800-129780400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr4:129763800-129780400	Strong transcription	Duodenum Mucosa	Duodenum

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