Variant report

Variant	rs4802207
Chromosome Location	chr19:44600377-44600378
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	FOXA1	chr19:44600377-44600584	T-47D	breast:	n/a	n/a
2	FOXA1	chr19:44600308-44600639	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44596713..44600957-chr19:44644435..44647275,5	MCF-7	breast:
2	chr19:44555396..44557599-chr19:44598429..44600981,2	MCF-7	breast:

Variant related genes	Relation type
ZNF224	TF binding region
ENSG00000178386	Chromatin interaction
ENSG00000263002	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10406335	0.81[CHB][hapmap]
rs10408901	0.81[CHB][hapmap]
rs10410306	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10420143	1.00[ASN][1000 genomes]
rs10853771	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1236715	0.88[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes]
rs1236716	0.88[CEU][hapmap];0.81[CHB][hapmap];0.80[GIH][hapmap];0.92[TSI][hapmap]
rs2061332	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2061333	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2284980	0.81[CHB][hapmap]
rs2284981	0.88[CEU][hapmap];0.81[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28446946	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28539456	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3172	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3200505	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3746319	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3746321	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4239529	0.82[CHB][hapmap]
rs4429390	0.83[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs4459653	0.83[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs4508518	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4802204	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4802205	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4802208	0.87[CEU][hapmap]
rs4803676	0.82[CHB][hapmap]
rs4803681	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55876899	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56353321	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62115524	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62115526	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250004	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7250005	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7508149	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8099869	0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8104573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8105860	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8108021	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8108404	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8113750	0.98[ASN][1000 genomes]
rs9304638	0.81[CHB][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	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4802207	SNRPD2	cis	cerebellum	SCAN
rs4802207	KLK10	cis	cerebellum	SCAN
rs4802207	ZNF221	cis	Lymphoblastoid	GTEx
rs4802207	FUT2	cis	parietal	SCAN
rs4802207	ZNF224	Cis_1M	lymphoblastoid	RTeQTL
rs4802207	SNORD34	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44598000-44600600	Active TSS	GM12878-XiMat	blood
2	chr19:44599600-44600400	Flanking Active TSS	Dnd41	blood
3	chr19:44599600-44601000	Weak transcription	Aorta	Aorta
4	chr19:44599600-44601800	Weak transcription	Gastric	stomach
5	chr19:44599600-44601800	Weak transcription	Pancreas	Pancrea
6	chr19:44599600-44602600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:44599600-44604400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:44599600-44604400	Weak transcription	Spleen	Spleen
9	chr19:44599600-44604800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:44599600-44608000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:44599600-44609000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:44599600-44610600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr19:44599600-44611000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:44599800-44600400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr19:44599800-44600400	Weak transcription	Brain Anterior Caudate	brain
16	chr19:44599800-44600400	Weak transcription	HSMM	muscle
17	chr19:44599800-44600400	Weak transcription	HSMMtube	muscle
18	chr19:44599800-44600600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr19:44599800-44600600	Enhancers	Primary T cells fromperipheralblood	blood
20	chr19:44599800-44600600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr19:44599800-44600600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:44599800-44600600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr19:44599800-44600600	Enhancers	Adipose Nuclei	Adipose
24	chr19:44599800-44600600	Enhancers	Fetal Muscle Leg	muscle
25	chr19:44599800-44600800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr19:44599800-44600800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr19:44599800-44600800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr19:44599800-44600800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr19:44599800-44600800	Weak transcription	Fetal Lung	lung
30	chr19:44599800-44600800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr19:44599800-44600800	Weak transcription	NHDF-Ad	bronchial
32	chr19:44599800-44601000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr19:44599800-44601000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr19:44599800-44601000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr19:44599800-44601000	Enhancers	Colon Smooth Muscle	Colon
36	chr19:44599800-44601000	Weak transcription	Left Ventricle	heart
37	chr19:44599800-44601000	Weak transcription	HMEC	breast
38	chr19:44599800-44601200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr19:44599800-44601200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:44599800-44601400	Weak transcription	Brain Angular Gyrus	brain
41	chr19:44599800-44601400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:44599800-44601400	Weak transcription	Brain Substantia Nigra	brain
43	chr19:44599800-44601600	Weak transcription	Fetal Kidney	kidney
44	chr19:44599800-44601800	Weak transcription	Fetal Stomach	stomach
45	chr19:44599800-44601800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr19:44599800-44601800	Weak transcription	Osteobl	bone
47	chr19:44599800-44602400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:44599800-44602600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:44599800-44604400	Weak transcription	Psoas Muscle	Psoas
50	chr19:44599800-44604600	Weak transcription	H1 Cell Line	embryonic stem cell

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