Variant report

Variant	rs2293229
Chromosome Location	chr4:8407406-8407407
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	chr4:8405868..8408180-chr4:8410385..8411900,2	K562	blood:
2	chr4:8404879..8407755-chr4:8409696..8411552,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10016221	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10017177	0.99[ASN][1000 genomes]
rs1006113	0.95[ASN][1000 genomes]
rs10938710	0.84[ASN][1000 genomes]
rs10938712	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11721377	0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11724408	0.95[ASN][1000 genomes]
rs11731308	0.95[ASN][1000 genomes]
rs11931965	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11934603	0.92[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs11938364	0.92[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs13103946	0.95[ASN][1000 genomes]
rs13107329	0.95[ASN][1000 genomes]
rs13130336	0.94[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13134272	0.92[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs13136987	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs13139522	0.92[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs13150818	0.93[ASN][1000 genomes]
rs1568692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1568693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242483	0.84[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs2293230	1.00[ASW][hapmap];0.92[LWK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs2386119	0.92[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap]
rs28541824	0.82[AFR][1000 genomes]
rs28637781	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28805000	0.95[ASN][1000 genomes]
rs34947973	0.96[ASN][1000 genomes]
rs35893558	0.96[ASN][1000 genomes]
rs3796740	0.92[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3796747	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs3796749	0.87[AFR][1000 genomes]
rs3822207	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs4543095	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6447868	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73087705	0.93[ASN][1000 genomes]
rs7668735	0.95[ASN][1000 genomes]
rs7696306	0.92[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs7697154	1.00[ASW][hapmap];0.89[LWK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs9291391	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9291392	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs940135	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs950306	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv878609	chr4:8373832-8407406	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv878610	chr4:8377058-8416976	ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv470014	chr4:8390646-8429817	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv593639	chr4:8394376-8424108	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2293229	C4orf23	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8366400-8411600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr4:8383800-8419000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:8384800-8418600	Strong transcription	Primary T cells from cord blood	blood
4	chr4:8385200-8411600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr4:8386400-8408400	Strong transcription	Fetal Intestine Large	intestine
6	chr4:8387400-8412000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:8389800-8411400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:8394800-8409400	Weak transcription	Small Intestine	intestine
9	chr4:8395800-8411800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:8396600-8419400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:8396800-8412400	Weak transcription	Fetal Brain Male	brain
12	chr4:8396800-8415600	Weak transcription	NH-A	brain
13	chr4:8397600-8409400	Weak transcription	HepG2	liver
14	chr4:8397600-8420400	Weak transcription	NHDF-Ad	bronchial
15	chr4:8398200-8409400	Weak transcription	Primary B cells from cord blood	blood
16	chr4:8399200-8412000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:8399400-8411800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:8399400-8412000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr4:8399600-8412000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:8399600-8429400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:8402800-8408400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr4:8403000-8408200	Strong transcription	Fetal Brain Female	brain
23	chr4:8403000-8408200	Strong transcription	Pancreas	Pancrea
24	chr4:8403200-8419400	Strong transcription	Fetal Intestine Small	intestine
25	chr4:8403400-8411400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:8403400-8414400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:8403600-8412200	Strong transcription	Brain Germinal Matrix	brain
28	chr4:8404000-8408000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:8404200-8408200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr4:8404200-8408400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:8404200-8408400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:8404400-8410000	Weak transcription	NHLF	lung
33	chr4:8404600-8411800	Weak transcription	NHEK	skin
34	chr4:8404600-8429400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr4:8404800-8407800	Strong transcription	Fetal Stomach	stomach
36	chr4:8404800-8411400	Weak transcription	Right Atrium	heart
37	chr4:8404800-8420600	Weak transcription	Psoas Muscle	Psoas
38	chr4:8405000-8407600	Strong transcription	Colonic Mucosa	Colon
39	chr4:8405000-8408200	Strong transcription	HSMM	muscle
40	chr4:8405000-8411200	Weak transcription	HMEC	breast
41	chr4:8405000-8412200	Weak transcription	HUVEC	blood vessel
42	chr4:8405000-8415600	Weak transcription	Fetal Kidney	kidney
43	chr4:8405200-8408400	Strong transcription	Brain Angular Gyrus	brain
44	chr4:8405200-8410600	Strong transcription	HSMMtube	muscle
45	chr4:8405200-8411800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr4:8405200-8412200	Strong transcription	Spleen	Spleen
47	chr4:8405400-8408000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:8405400-8408200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:8405400-8408200	Strong transcription	Brain Anterior Caudate	brain
50	chr4:8405400-8408200	Strong transcription	Rectal Smooth Muscle	rectum

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