Variant report

Variant	rs228618
Chromosome Location	chr4:103567348-103567349
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103566516..103568311-chr4:103572025..103574131,2	MCF-7	breast:
2	chr4:103567141..103568806-chr4:103583001..103584546,2	K562	blood:

Variant related genes	Relation type
ENSG00000241981	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1054029	0.81[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap]
rs1054037	0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs1077358	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11724614	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11727546	0.84[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12498722	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12644381	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs13106304	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs13106325	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs17033015	0.86[JPT][hapmap]
rs179195	0.89[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs2125211	0.82[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap]
rs2272695	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2272696	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2272697	0.81[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs227276	0.85[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs227277	0.85[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs227361	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs228611	0.89[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs228614	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs228617	0.94[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap]
rs228619	0.88[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap]
rs228623	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap]
rs2866407	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2866412	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2866413	0.81[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs2866414	0.81[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs2903283	0.86[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs3733202	0.84[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs4013	0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs404574	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs434644	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs4496586	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4547797	0.81[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs4586937	0.81[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs5026472	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs5026473	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs5026474	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs5026476	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6533020	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6533021	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6810869	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6812747	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6839064	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs735403	0.81[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs735404	0.81[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs735405	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7674640	0.81[CHB][hapmap]
rs7677509	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7699231	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7699678	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs909349	0.81[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][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	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	esv1799158	chr4:103556316-103580296	Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1008110	chr4:103560583-103684526	Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs228618	CISD2	cis	parietal	SCAN
rs228618	RG9MTD2	cis	cerebellum	SCAN
rs228618	ADH7	cis	cerebellum	SCAN
rs228618	MANBA	cis	parietal	SCAN
rs228618	CISD2	cis	lymphoblastoid	seeQTL
rs228618	MANBA	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103536200-103595400	Weak transcription	Colonic Mucosa	Colon
2	chr4:103536600-103595800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:103541800-103571000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:103542400-103578800	Weak transcription	Psoas Muscle	Psoas
5	chr4:103542400-103594400	Weak transcription	K562	blood
6	chr4:103542400-103617400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:103545200-103592000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:103547000-103658200	Weak transcription	Small Intestine	intestine
9	chr4:103549000-103570400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:103549800-103572000	Weak transcription	Placenta	Placenta
11	chr4:103550200-103582800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:103550400-103573000	Weak transcription	Fetal Kidney	kidney
13	chr4:103551000-103607600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr4:103551000-103607800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr4:103552400-103579600	Weak transcription	Fetal Heart	heart
16	chr4:103553000-103651400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr4:103553200-103591200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:103553400-103567800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:103553400-103568000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr4:103553400-103568800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:103553400-103608200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:103553400-103651400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:103554600-103567800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr4:103556000-103570400	Weak transcription	Fetal Brain Female	brain
25	chr4:103556000-103593800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:103556200-103571200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:103556200-103572800	Weak transcription	Right Ventricle	heart
28	chr4:103556200-103581000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:103556200-103581000	Weak transcription	Gastric	stomach
30	chr4:103556200-103582200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:103556200-103588600	Weak transcription	Esophagus	oesophagus
32	chr4:103556200-103650400	Weak transcription	Pancreas	Pancrea
33	chr4:103556600-103569400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr4:103557200-103573600	Weak transcription	A549	lung
35	chr4:103557600-103585200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:103557600-103626400	Weak transcription	Lung	lung
37	chr4:103558800-103569000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:103558800-103569400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:103558800-103569800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr4:103559200-103571000	Weak transcription	HepG2	liver
41	chr4:103559200-103590000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr4:103559600-103617200	Weak transcription	Fetal Stomach	stomach
43	chr4:103559800-103569800	Weak transcription	Fetal Lung	lung
44	chr4:103560000-103595400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr4:103560400-103570800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr4:103560600-103584000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr4:103560800-103569600	Weak transcription	Fetal Intestine Large	intestine
48	chr4:103560800-103571200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:103560800-103585200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:103560800-103587800	Weak transcription	Colon Smooth Muscle	Colon

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