Variant report

Variant	rs2288549
Chromosome Location	chr7:128044035-128044036
allele	C/T
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	NR3C1	chr7:128043947-128044886	A549	lung:	n/a	chr7:128044361-128044368 chr7:128044611-128044625 chr7:128044415-128044433 chr7:128044287-128044296 chr7:128044610-128044626 chr7:128044607-128044628 chr7:128044326-128044339 chr7:128044416-128044431 chr7:128044609-128044627
2	HEY1	chr7:128043584-128044884	K562	blood:	n/a	n/a
3	POLR2A	chr7:128043796-128044779	K562	blood:	n/a	n/a
4	NR3C1	chr7:128044026-128044868	A549	lung:	n/a	chr7:128044361-128044368 chr7:128044611-128044625 chr7:128044415-128044433 chr7:128044287-128044296 chr7:128044610-128044626 chr7:128044607-128044628 chr7:128044326-128044339 chr7:128044416-128044431 chr7:128044609-128044627

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:127999383..128002185-chr7:128042634..128044178,2	K562	blood:
2	chr7:127981986..127985324-chr7:128043786..128047324,3	K562	blood:

Variant related genes	Relation type
IMPDH1	TF binding region
ENSG00000238750	Chromatin interaction
ENSG00000106344	Chromatin interaction
ENSG00000224940	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10229016	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10229394	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10230965	1.00[JPT][hapmap]
rs10251597	1.00[JPT][hapmap]
rs1035971	0.91[TSI][hapmap]
rs1065267	0.88[CEU][hapmap]
rs11770116	1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs11980741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12672625	1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs13245629	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs1560214	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17537088	0.82[CEU][hapmap]
rs2288548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2402892	0.91[TSI][hapmap]
rs2402895	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562730	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2562733	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2562734	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2562737	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs2562740	1.00[JPT][hapmap]
rs2732394	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2732397	0.83[AMR][1000 genomes]
rs2732429	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3097361	0.81[AMR][1000 genomes]
rs4728108	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4731446	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4731448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731450	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731454	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4731455	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6467178	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6947697	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6948333	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs930106	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831124	chr7:127970345-128147910	Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv889191	chr7:127973133-128073326	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv608400	chr7:127978820-128048194	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
4	esv2493565	chr7:127985695-128053377	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3478325	chr7:127986726-128053483	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv3478326	chr7:127986726-128053483	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv515737	chr7:128044035-128050417	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2288549	IL31RA	trans	parietal	SCAN
rs2288549	ZNF800	cis	parietal	SCAN
rs2288549	TMEM209	cis	parietal	SCAN
rs2288549	FAM71F2	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128002400-128044400	Weak transcription	Right Atrium	heart
2	chr7:128028000-128045200	Weak transcription	Small Intestine	intestine
3	chr7:128028400-128044600	Weak transcription	Fetal Heart	heart
4	chr7:128029600-128044400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:128031200-128044200	Strong transcription	Spleen	Spleen
6	chr7:128031400-128044200	Strong transcription	Fetal Muscle Leg	muscle
7	chr7:128031600-128044400	Strong transcription	Fetal Intestine Small	intestine
8	chr7:128034800-128044200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:128038200-128044200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:128038400-128045200	Weak transcription	Fetal Kidney	kidney
11	chr7:128039000-128044400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr7:128040800-128044600	Weak transcription	Fetal Intestine Large	intestine
13	chr7:128041000-128044800	Weak transcription	Brain Hippocampus Middle	brain
14	chr7:128041000-128045000	Weak transcription	Liver	Liver
15	chr7:128041200-128045000	Weak transcription	Brain Angular Gyrus	brain
16	chr7:128041400-128044200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:128041400-128044200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr7:128041400-128044200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr7:128041400-128044200	Weak transcription	Esophagus	oesophagus
20	chr7:128041400-128044200	Weak transcription	Thymus	Thymus
21	chr7:128041400-128045000	Weak transcription	Aorta	Aorta
22	chr7:128041600-128044400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:128041600-128044400	Weak transcription	Fetal Thymus	thymus
24	chr7:128041600-128044400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr7:128041600-128044400	Weak transcription	HSMMtube	muscle
26	chr7:128041600-128045000	Weak transcription	Ovary	ovary
27	chr7:128041800-128044200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr7:128041800-128044200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:128041800-128044200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:128041800-128044200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr7:128041800-128044200	Weak transcription	Colonic Mucosa	Colon
32	chr7:128041800-128044200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr7:128041800-128044400	Weak transcription	Placenta	Placenta
34	chr7:128041800-128045000	Weak transcription	Brain Cingulate Gyrus	brain
35	chr7:128042000-128044200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr7:128042000-128044200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr7:128042000-128044400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr7:128042000-128044400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr7:128042000-128044400	Weak transcription	Right Ventricle	heart
40	chr7:128042200-128045000	Weak transcription	Brain Substantia Nigra	brain
41	chr7:128042800-128045000	Enhancers	Fetal Lung	lung
42	chr7:128043000-128044200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr7:128043000-128044200	Enhancers	Brain Germinal Matrix	brain
44	chr7:128043000-128044200	Weak transcription	NHLF	lung
45	chr7:128043000-128044400	Weak transcription	NHDF-Ad	bronchial
46	chr7:128043200-128044200	Weak transcription	Gastric	stomach
47	chr7:128043200-128044200	Weak transcription	A549	lung
48	chr7:128043200-128044200	Weak transcription	Osteobl	bone
49	chr7:128043200-128044600	Weak transcription	Primary T cells from cord blood	blood
50	chr7:128043200-128044800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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