Variant report

Variant	rs4233235
Chromosome Location	chr1:224520447-224520448
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224516510..224520785-chr1:224542312..224545237,4	MCF-7	breast:
2	chr1:224299141..224303224-chr1:224514971..224520507,6	MCF-7	breast:
3	chr1:224518917..224520505-chr1:224603119..224605851,2	K562	blood:
4	chr1:224301568..224304233-chr1:224516678..224521021,7	MCF-7	breast:
5	chr1:224518317..224520601-chr1:224521846..224526256,3	K562	blood:
6	chr1:224376961..224379372-chr1:224517838..224520632,2	K562	blood:

Variant related genes	Relation type
ENSG00000143771	Chromatin interaction
ENSG00000143753	Chromatin interaction
ENSG00000143756	Chromatin interaction
ENSG00000238856	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10158063	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10753462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10753464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10799562	0.85[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap]
rs10799575	0.80[YRI][hapmap]
rs10916585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1573088	0.80[YRI][hapmap]
rs16846031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs16846094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16846214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs16846244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1806742	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2404783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2404861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2405048	0.80[YRI][hapmap]
rs2405065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs2896990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs3754090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs3767721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs3767722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs3767723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs3767724	1.00[JPT][hapmap]
rs4146965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4146966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4233234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4256779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs4653579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4653580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4653581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4653584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs4654017	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs4654019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4654022	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4654023	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs6426088	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6426094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6426100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs6426110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6426124	0.80[YRI][hapmap]
rs6681790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs6682667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs6694310	0.80[YRI][hapmap]
rs6694745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7521015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs7530205	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs7534101	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap]
rs7534447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9287027	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]

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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4233235	NVL	cis	multi-tissue	Pritchard

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224518600-224526200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:224518600-224528600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:224518800-224521000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:224518800-224521000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:224518800-224521000	Weak transcription	Primary T cells from cord blood	blood
6	chr1:224518800-224521000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:224518800-224521000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:224518800-224521000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:224518800-224521000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:224518800-224521000	Weak transcription	HSMM	muscle
11	chr1:224518800-224521200	Weak transcription	NHLF	lung
12	chr1:224518800-224521400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:224518800-224521400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:224518800-224521400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:224518800-224521400	Weak transcription	NH-A	brain
16	chr1:224518800-224521600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:224519000-224520800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:224519000-224520800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr1:224519000-224520800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:224519000-224520800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:224519000-224520800	Weak transcription	K562	blood
22	chr1:224519000-224521000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:224519000-224521000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:224519000-224521000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:224519000-224521000	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:224519000-224521000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:224519000-224521000	Weak transcription	A549	lung
28	chr1:224519000-224521000	Weak transcription	GM12878-XiMat	blood
29	chr1:224519000-224521000	Weak transcription	NHEK	skin
30	chr1:224519000-224521200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:224519000-224521200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:224519000-224521200	Weak transcription	HUVEC	blood vessel
33	chr1:224519000-224521200	Weak transcription	NHDF-Ad	bronchial
34	chr1:224519000-224521200	Weak transcription	Osteobl	bone
35	chr1:224519000-224521400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:224519000-224521400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:224519000-224521400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:224519000-224521400	Weak transcription	HMEC	breast
39	chr1:224519000-224521400	Weak transcription	HSMMtube	muscle
40	chr1:224519000-224521800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:224519200-224520800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:224519200-224520800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr1:224519200-224521000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr1:224519200-224521000	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:224519200-224521000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:224519200-224521000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:224519200-224521200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr1:224519200-224521400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:224519200-224521400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:224519200-224526200	Weak transcription	HepG2	liver

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