Variant report

Variant	rs223420
Chromosome Location	chr4:103728010-103728011
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:103727967-103729385	K562	blood:	n/a	n/a
2	POLR2A	chr4:103727890-103728068	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr4:103727768-103728487	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:103722794-103729937	HepG2	liver:	n/a	n/a
5	POLR2A	chr4:103727931-103728652	K562	blood:	n/a	n/a
6	POLR2A	chr4:103727916-103728451	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103727572..103730495-chr4:103786922..103788552,2	MCF-7	breast:
2	chr4:100867650..100870062-chr4:103727298..103729005,2	K562	blood:
3	chr4:103717056..103718785-chr4:103726138..103728773,2	K562	blood:

Variant related genes	Relation type
UBE2D3	TF binding region
ENSG00000164031	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10003326	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs10012413	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10015289	0.90[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap]
rs11097796	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs11722779	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs11737544	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs12500379	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs12508069	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs1383733	0.88[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs150893	0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap]
rs150895	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs17033381	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223308	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs223313	0.91[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap]
rs223314	0.95[CEU][hapmap]
rs223315	0.84[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs223318	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs223324	0.90[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap]
rs223326	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223330	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223334	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs223338	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223339	0.85[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs223346	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223347	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223349	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223350	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs223353	0.90[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap]
rs223356	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223358	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223359	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs223363	0.85[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs223367	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs223381	0.88[CEU][hapmap]
rs223383	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs223385	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs223390	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223392	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223395	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs223397	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs223400	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs223401	0.91[JPT][hapmap]
rs223410	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs223412	0.88[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap]
rs223418	0.90[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap]
rs223419	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223425	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223438	0.89[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap]
rs223441	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs223446	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs223447	0.90[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap]
rs223448	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs223450	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223452	0.90[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.84[YRI][hapmap]
rs223454	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs223457	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs223458	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap]
rs223461	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs223467	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs223474	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223475	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs223484	0.90[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap]
rs223486	0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs223497	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs223498	0.89[ASW][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap]
rs2866417	0.88[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs3774987	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs3886722	0.88[CEU][hapmap]
rs3886723	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs3974485	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs3974604	0.90[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap]
rs3974608	0.88[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs4623004	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs5028609	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6419160	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs6533041	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6533050	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs6533051	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6533052	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs65671	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap]
rs6810668	0.82[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap]
rs6815526	0.89[ASW][hapmap];0.84[YRI][hapmap]
rs6823625	0.84[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs6824070	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs6846762	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs6852141	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap]
rs6853193	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7254	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap]
rs7663876	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7672319	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs7676943	0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs7681629	0.90[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap]
rs7685399	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs9307281	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs9999303	0.90[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526256	chr4:103712589-103728010	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs223420	KRT8P46	cis	lung	GTEx
rs223420	CISD2	cis	parietal	SCAN
rs223420	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs223420	CISD2	cis	Esophagus Muscularis	GTEx
rs223420	CISD2	cis	cerebellum	SCAN
rs223420	CISD2	cis	multi-tissue	Pritchard
rs223420	CISD2	cis	Skin Sun Exposed Lower leg	GTEx
rs223420	MANBA	cis	parietal	SCAN
rs223420	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs223420	CISD2	cis	Nerve Tibial	GTEx
rs223420	MANBA	cis	multi-tissue	Pritchard
rs223420	LRRC37A15P	cis	lung	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	chr4:103711800-103728400	Strong transcription	HSMM	muscle
7	chr4:103712400-103729200	Strong transcription	Muscle Satellite Cultured Cells	--
8	chr4:103712400-103730000	Strong transcription	Primary hematopoietic stem cells	blood
9	chr4:103712400-103735000	Strong transcription	K562	blood
10	chr4:103712400-103736200	Strong transcription	Fetal Intestine Large	intestine
11	chr4:103712400-103737200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:103712600-103729000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:103712600-103729800	Strong transcription	Adipose Nuclei	Adipose
14	chr4:103712600-103730200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:103712600-103730400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:103712600-103731200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:103712600-103739600	Strong transcription	Fetal Thymus	thymus
18	chr4:103712800-103730600	Strong transcription	Primary B cells from cord blood	blood
19	chr4:103712800-103730800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:103712800-103730800	Strong transcription	NH-A	brain
21	chr4:103712800-103731600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr4:103712800-103736800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:103713000-103744400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:103713600-103730800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:103714000-103730400	Strong transcription	GM12878-XiMat	blood
26	chr4:103714000-103732200	Weak transcription	Esophagus	oesophagus
27	chr4:103714000-103740800	Weak transcription	Aorta	Aorta
28	chr4:103714800-103728200	Strong transcription	Liver	Liver
29	chr4:103714800-103729400	Strong transcription	HUVEC	blood vessel
30	chr4:103714800-103733200	Strong transcription	Duodenum Mucosa	Duodenum
31	chr4:103714800-103737200	Strong transcription	Dnd41	blood
32	chr4:103715200-103732200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:103715600-103730400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr4:103715600-103730800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr4:103715600-103731600	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:103715800-103728600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:103715800-103730400	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr4:103716000-103731000	Strong transcription	Placenta	Placenta
39	chr4:103716000-103736000	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr4:103716200-103730400	Strong transcription	HMEC	breast
41	chr4:103716200-103730800	Strong transcription	NHEK	skin
42	chr4:103716400-103731200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr4:103716600-103732200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:103716800-103728200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr4:103717000-103729800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:103717400-103731400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:103717400-103732200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:103717400-103732200	Weak transcription	Gastric	stomach
49	chr4:103718200-103731200	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:103718200-103731200	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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