Variant report

Variant	rs227369
Chromosome Location	chr4:103612018-103612019
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103603495..103606778-chr4:103609035..103613209,7	K562	blood:
2	chr4:103603807..103606307-chr4:103609358..103612973,3	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13112128	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs170563	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap]
rs170564	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs223391	0.80[JPT][hapmap]
rs223408	0.80[JPT][hapmap]
rs223495	0.93[JPT][hapmap]
rs223496	0.93[JPT][hapmap]
rs223499	0.93[JPT][hapmap]
rs223500	0.93[JPT][hapmap]
rs223501	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs223502	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs223504	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs223505	0.95[CEU][hapmap]
rs223508	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs223510	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs223512	0.87[CEU][hapmap]
rs227280	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs227283	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.97[TSI][hapmap]
rs227284	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs227285	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs227370	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs227372	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs393223	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][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	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
2	nsv1013963	chr4:103606672-103645082	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs227369	KRT8P46	cis	lung	GTEx
rs227369	CISD2	cis	lymphoblastoid	seeQTL
rs227369	CISD2	cis	Temporal Cortex	GTEx
rs227369	MANBA	cis	lymphoblastoid	seeQTL
rs227369	MANBA	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103542400-103617400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:103547000-103658200	Weak transcription	Small Intestine	intestine
3	chr4:103553000-103651400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:103553400-103651400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:103556200-103650400	Weak transcription	Pancreas	Pancrea
6	chr4:103557600-103626400	Weak transcription	Lung	lung
7	chr4:103559600-103617200	Weak transcription	Fetal Stomach	stomach
8	chr4:103561000-103614600	Weak transcription	Fetal Muscle Leg	muscle
9	chr4:103563400-103617600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:103570800-103618000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:103571800-103633600	Weak transcription	HepG2	liver
12	chr4:103571800-103655800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:103572000-103640800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr4:103572800-103612600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr4:103579400-103615000	Weak transcription	Psoas Muscle	Psoas
16	chr4:103580000-103644000	Weak transcription	Aorta	Aorta
17	chr4:103580400-103640600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr4:103581200-103627000	Weak transcription	Gastric	stomach
19	chr4:103581800-103681000	Weak transcription	Spleen	Spleen
20	chr4:103585600-103613800	Weak transcription	Fetal Intestine Large	intestine
21	chr4:103586000-103640600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr4:103589000-103618000	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:103590000-103626200	Weak transcription	Ovary	ovary
24	chr4:103590200-103616800	Weak transcription	Fetal Lung	lung
25	chr4:103594200-103614000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr4:103594400-103617400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:103594400-103624200	Weak transcription	Fetal Intestine Small	intestine
28	chr4:103594600-103612200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:103595200-103617400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr4:103595800-103613800	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr4:103596200-103640600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr4:103602400-103624800	Weak transcription	Placenta	Placenta
33	chr4:103604000-103617600	Weak transcription	Fetal Brain Male	brain
34	chr4:103604200-103616000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:103604200-103616800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr4:103604200-103626400	Weak transcription	Right Ventricle	heart
37	chr4:103604400-103617800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:103605600-103613400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:103606000-103614600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:103606000-103617000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:103606000-103626600	Weak transcription	Left Ventricle	heart
42	chr4:103606200-103612600	Weak transcription	Dnd41	blood
43	chr4:103606200-103614000	Weak transcription	Primary T cells from cord blood	blood
44	chr4:103606800-103613600	Weak transcription	NHLF	lung
45	chr4:103608800-103644600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:103609200-103615800	Weak transcription	NHDF-Ad	bronchial
47	chr4:103609200-103617400	Strong transcription	Primary B cells from cord blood	blood
48	chr4:103609200-103617600	Weak transcription	HSMMtube	muscle
49	chr4:103609200-103618600	Weak transcription	Brain Substantia Nigra	brain
50	chr4:103609200-103619000	Weak transcription	Duodenum Mucosa	Duodenum

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