Variant report

Variant	rs223419
Chromosome Location	chr4:103729743-103729744
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103727572..103730495-chr4:103786922..103788552,2	MCF-7	breast:
2	chr4:103729408..103730314-chr8:87178649..87179164,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10003326	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs10012413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10015289	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs11097796	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11722779	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs11737544	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12500379	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs12508069	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs1383733	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs150893	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs150895	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs17033381	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap]
rs223308	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223313	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs223314	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs223315	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223318	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223334	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223338	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs223339	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223346	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223347	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223350	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs223353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223359	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223363	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223367	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223381	1.00[CEU][hapmap]
rs223383	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs223385	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223395	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap]
rs223397	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs223400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs223401	0.91[JPT][hapmap]
rs223410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223412	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs223420	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223441	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223448	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223454	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223457	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs223461	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs223467	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223474	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223475	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223484	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223486	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs223497	0.89[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs2866417	0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs3774987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3886722	0.93[CEU][hapmap]
rs3886723	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs3974485	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3974604	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs3974608	0.93[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4623004	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs5028609	0.93[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs6419160	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6533041	0.93[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs6533050	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6533051	0.92[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs6533052	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs65671	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6810668	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap]
rs6815526	1.00[YRI][hapmap]
rs6823625	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs6824070	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs6846762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6852141	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs6853193	0.96[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap]
rs7254	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7663876	0.93[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap]
rs7672319	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7676943	0.93[CEU][hapmap];0.96[CHB][hapmap];0.86[JPT][hapmap]
rs7681629	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap]
rs7685399	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs9307281	0.96[CHB][hapmap];0.91[JPT][hapmap]
rs9999303	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594957	chr4:103728010-103870091	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs223419	CISD2	cis	Nerve Tibial	GTEx
rs223419	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs223419	CISD2	cis	Skin Sun Exposed Lower leg	GTEx
rs223419	MANBA	cis	multi-tissue	Pritchard
rs223419	LRRC37A15P	cis	lung	GTEx
rs223419	KRT8P46	cis	lung	GTEx
rs223419	CISD2	cis	multi-tissue	Pritchard
rs223419	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs223419	CISD2	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103700600-103731600	Weak transcription	Pancreas	Pancrea
2	chr4:103707800-103732200	Weak transcription	Right Ventricle	heart
3	chr4:103711200-103731000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:103711200-103731600	Weak transcription	Spleen	Spleen
5	chr4:103711400-103732600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:103712400-103730000	Strong transcription	Primary hematopoietic stem cells	blood
7	chr4:103712400-103735000	Strong transcription	K562	blood
8	chr4:103712400-103736200	Strong transcription	Fetal Intestine Large	intestine
9	chr4:103712400-103737200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:103712600-103729800	Strong transcription	Adipose Nuclei	Adipose
11	chr4:103712600-103730200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:103712600-103730400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:103712600-103731200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:103712600-103739600	Strong transcription	Fetal Thymus	thymus
15	chr4:103712800-103730600	Strong transcription	Primary B cells from cord blood	blood
16	chr4:103712800-103730800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:103712800-103730800	Strong transcription	NH-A	brain
18	chr4:103712800-103731600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:103712800-103736800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:103713000-103744400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:103713600-103730800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr4:103714000-103730400	Strong transcription	GM12878-XiMat	blood
23	chr4:103714000-103732200	Weak transcription	Esophagus	oesophagus
24	chr4:103714000-103740800	Weak transcription	Aorta	Aorta
25	chr4:103714800-103733200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr4:103714800-103737200	Strong transcription	Dnd41	blood
27	chr4:103715200-103732200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:103715600-103730400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr4:103715600-103730800	Strong transcription	Primary B cells from peripheral blood	blood
30	chr4:103715600-103731600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:103715800-103730400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr4:103716000-103731000	Strong transcription	Placenta	Placenta
33	chr4:103716000-103736000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr4:103716200-103730400	Strong transcription	HMEC	breast
35	chr4:103716200-103730800	Strong transcription	NHEK	skin
36	chr4:103716400-103731200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr4:103716600-103732200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:103717000-103729800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:103717400-103731400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:103717400-103732200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:103717400-103732200	Weak transcription	Gastric	stomach
42	chr4:103718200-103731200	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr4:103718200-103731200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr4:103718200-103739200	Weak transcription	Stomach Mucosa	stomach
45	chr4:103718400-103731800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr4:103718400-103732000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr4:103719200-103732000	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:103719200-103733200	Weak transcription	Psoas Muscle	Psoas
49	chr4:103719800-103733200	Weak transcription	Small Intestine	intestine
50	chr4:103720000-103732400	Weak transcription	Fetal Brain Male	brain

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