Variant report

Variant	rs230534
Chromosome Location	chr4:103449041-103449042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103447755..103449902-chr4:103466038..103467792,2	K562	blood:
2	chr4:103442159..103444303-chr4:103446884..103449201,2	MCF-7	breast:
3	chr4:103422268..103425518-chr4:103448711..103450558,3	MCF-7	breast:
4	chr4:103422449..103425804-chr4:103447009..103450716,4	K562	blood:

Variant related genes	Relation type
ENSG00000260651	Chromatin interaction
ENSG00000109320	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1005819	0.91[JPT][hapmap]
rs1020760	0.91[JPT][hapmap]
rs11722146	0.80[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs11723120	0.83[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs118882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12509517	0.80[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs12648696	0.88[CHB][hapmap]
rs1585213	1.00[JPT][hapmap]
rs1585215	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1598859	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1599961	1.00[JPT][hapmap]
rs17032683	1.00[YRI][hapmap]
rs17032705	1.00[JPT][hapmap]
rs170731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1801	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2085549	1.00[YRI][hapmap]
rs2168805	0.95[JPT][hapmap]
rs230491	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230492	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230493	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230495	1.00[JPT][hapmap]
rs230496	1.00[JPT][hapmap]
rs230498	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230500	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230504	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230505	1.00[JPT][hapmap]
rs230509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230511	1.00[CEU][hapmap]
rs230514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230521	1.00[JPT][hapmap]
rs230525	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230526	1.00[JPT][hapmap]
rs230528	1.00[JPT][hapmap]
rs230529	1.00[JPT][hapmap]
rs230531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230533	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230535	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230539	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs230540	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs230541	0.90[JPT][hapmap]
rs230542	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2903281	1.00[YRI][hapmap]
rs3755867	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs3774933	1.00[JPT][hapmap]
rs3774936	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3774937	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3774938	1.00[JPT][hapmap]
rs3774956	0.95[JPT][hapmap]
rs3774959	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3774963	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3774964	0.90[JPT][hapmap]
rs3817685	0.95[JPT][hapmap]
rs3821958	0.91[JPT][hapmap]
rs4235404	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4456957	1.00[YRI][hapmap]
rs4648011	1.00[JPT][hapmap]
rs4648055	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4648058	0.90[JPT][hapmap]
rs4648068	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4648085	1.00[YRI][hapmap]
rs4648133	0.87[CEU][hapmap]
rs4698858	0.89[JPT][hapmap]
rs4698861	0.82[CEU][hapmap]
rs4699030	0.90[JPT][hapmap]
rs747559	1.00[JPT][hapmap]
rs9790601	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs980455	1.00[JPT][hapmap]

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	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1003490	chr4:103391483-103521772	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1004030	chr4:103419352-103504042	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537203	chr4:103419352-103504042	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103425200-103456400	Weak transcription	Osteobl	bone
2	chr4:103426000-103452600	Weak transcription	NH-A	brain
3	chr4:103426000-103456400	Weak transcription	NHDF-Ad	bronchial
4	chr4:103426400-103450000	Weak transcription	HMEC	breast
5	chr4:103426400-103452600	Weak transcription	HSMMtube	muscle
6	chr4:103426400-103460800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr4:103428000-103449200	Weak transcription	Fetal Kidney	kidney
8	chr4:103433200-103466000	Weak transcription	Hela-S3	cervix
9	chr4:103440000-103459600	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:103440000-103460600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:103440000-103466200	Weak transcription	Aorta	Aorta
12	chr4:103440000-103484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:103440200-103451000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr4:103440200-103460600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr4:103440200-103473200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:103440200-103478600	Weak transcription	Right Ventricle	heart
17	chr4:103440200-103488200	Weak transcription	Gastric	stomach
18	chr4:103441400-103464200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:103441400-103469400	Weak transcription	Ovary	ovary
20	chr4:103441400-103482000	Weak transcription	Spleen	Spleen
21	chr4:103442400-103459600	Weak transcription	Fetal Stomach	stomach
22	chr4:103443000-103449200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:103443000-103455400	Weak transcription	HSMM	muscle
24	chr4:103443200-103449400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr4:103443200-103474200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:103443200-103496000	Weak transcription	A549	lung
27	chr4:103443400-103455400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:103443600-103450000	Weak transcription	NHEK	skin
29	chr4:103443800-103456800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:103444000-103459600	Weak transcription	Fetal Intestine Small	intestine
31	chr4:103444400-103470600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr4:103444600-103456000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:103444800-103458600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:103444800-103473000	Weak transcription	Small Intestine	intestine
35	chr4:103445000-103449200	Weak transcription	Fetal Heart	heart
36	chr4:103445000-103450000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr4:103445000-103450200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:103445000-103496600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:103445200-103449200	Weak transcription	Brain Anterior Caudate	brain
40	chr4:103445200-103470000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr4:103445600-103460400	Weak transcription	Dnd41	blood
42	chr4:103446000-103449800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
43	chr4:103446000-103456200	Strong transcription	Primary B cells from cord blood	blood
44	chr4:103446200-103449200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr4:103446200-103451000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:103446200-103455200	Weak transcription	Placenta	Placenta
47	chr4:103446200-103459000	Weak transcription	Left Ventricle	heart
48	chr4:103446200-103462800	Weak transcription	Esophagus	oesophagus
49	chr4:103446200-103462800	Weak transcription	Psoas Muscle	Psoas
50	chr4:103446200-103466000	Weak transcription	Lung	lung

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