Variant report

Variant	rs7781977
Chromosome Location	chr7:50346134-50346135
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	MYC	chr7:50346075-50347609	K562	blood:	n/a	chr7:50346561-50346571
2	MXI1	chr7:50346126-50347159	K562	blood:	n/a	n/a
3	IRF1	chr7:50345735-50347563	K562	blood:	n/a	n/a
4	CHD1	chr7:50345801-50348984	GM12878	blood:	n/a	n/a
5	NFIC	chr7:50345877-50347301	GM12878	blood:	n/a	n/a
6	MAX	chr7:50345708-50347563	NB4	blood:	n/a	chr7:50346561-50346571
7	POLR2A	chr7:50345612-50349306	HL-60	blood:	n/a	n/a
8	RUNX3	chr7:50345918-50347233	GM12878	blood:	n/a	n/a
9	POLR2A	chr7:50343739-50350920	GM12891	blood:	n/a	n/a
10	WRNIP1	chr7:50346108-50349128	GM12878	blood:	n/a	n/a
11	POLR2A	chr7:50346053-50347308	HL-60	blood:	n/a	n/a
12	UBTF	chr7:50345843-50349128	K562	blood:	n/a	n/a
13	MXI1	chr7:50346058-50347619	GM12878	blood:	n/a	n/a
14	POLR2A	chr7:50343378-50352747	GM12878	blood:	n/a	n/a
15	TEAD4	chr7:50345783-50347838	K562	blood:	n/a	chr7:50345844-50345853
16	POLR2A	chr7:50345709-50348424	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:50345514..50347628-chr7:50434884..50437361,2	MCF-7	breast:
2	chr7:50237645..50240143-chr7:50344951..50346541,2	K562	blood:
3	chr7:50245054..50247899-chr7:50345747..50347380,2	K562	blood:
4	chr7:50313753..50316737-chr7:50346108..50348567,2	K562	blood:
5	chr7:50345029..50346765-chr7:50447263..50449300,2	K562	blood:

Variant related genes	Relation type
IKZF1	TF binding region
ENSG00000235620	Chromatin interaction
ENSG00000185811	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10269380	0.81[AMR][1000 genomes]
rs11761922	0.80[AMR][1000 genomes]
rs11765436	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17732497	1.00[CEU][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1993444	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28625973	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4917017	0.83[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55957767	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62447179	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6421315	0.81[GIH][hapmap]
rs6583437	0.83[AMR][1000 genomes]
rs6583440	0.87[GIH][hapmap]
rs7791218	0.81[AMR][1000 genomes]
rs7805434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9886239	0.88[CEU][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464444	chr7:49671882-50454736	Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv606897	chr7:49671883-50454736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv498090	chr7:49708644-50427714	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1020869	chr7:49712860-50457544	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1024102	chr7:50195864-50418159	Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
IgG glycosylation	23382691	GWAS catalog

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50343000-50346600	Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr7:50343200-50346400	Active TSS	Primary T cells from cord blood	blood
3	chr7:50343200-50346400	Active TSS	Rectal Smooth Muscle	rectum
4	chr7:50343200-50347200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:50343200-50347400	Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr7:50343200-50347600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
7	chr7:50343400-50346200	Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr7:50343400-50346400	Active TSS	Primary monocytes fromperipheralblood	blood
9	chr7:50343400-50346400	Active TSS	Monocytes-CD14+_RO01746	blood
10	chr7:50343400-50346600	Active TSS	Dnd41	blood
11	chr7:50343400-50347000	Active TSS	Primary T cells fromperipheralblood	blood
12	chr7:50343400-50347000	Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr7:50343400-50347000	Active TSS	GM12878-XiMat	blood
14	chr7:50343400-50347200	Active TSS	Primary B cells from peripheral blood	blood
15	chr7:50343400-50347200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
16	chr7:50343400-50347400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:50343400-50347400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr7:50343400-50347400	Active TSS	Fetal Thymus	thymus
19	chr7:50343400-50347400	Active TSS	K562	blood
20	chr7:50343400-50347600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr7:50343400-50347800	Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr7:50343400-50348200	Active TSS	Thymus	Thymus
23	chr7:50343800-50346800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
24	chr7:50344000-50348400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:50344400-50347200	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr7:50344600-50346400	Bivalent/Poised TSS	Adipose Nuclei	Adipose
27	chr7:50344800-50346400	Bivalent/Poised TSS	Liver	Liver
28	chr7:50344800-50347400	Active TSS	Brain Hippocampus Middle	brain
29	chr7:50345000-50346200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr7:50345000-50346400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:50345200-50346400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
32	chr7:50345200-50348400	Weak transcription	Spleen	Spleen
33	chr7:50345400-50346400	Active TSS	Colonic Mucosa	Colon
34	chr7:50345400-50346400	Active TSS	Placenta	Placenta
35	chr7:50345400-50346400	Active TSS	Small Intestine	intestine
36	chr7:50345400-50346800	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr7:50345400-50347200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr7:50345400-50347400	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr7:50345400-50347800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr7:50345400-50351000	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr7:50345600-50346400	Active TSS	Right Atrium	heart
42	chr7:50345800-50347000	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr7:50346000-50349000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr7:50346000-50350400	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr7:50346000-50353000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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