Variant report

Variant	rs1250104
Chromosome Location	chr4:1196238-1196239
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	POLR2A	chr4:1194473-1196312	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:1195556-1196297	GM12878	blood:	n/a	n/a
3	ZNF143	chr4:1195846-1196307	GM12878	blood:	n/a	n/a
4	USF2	chr4:1195862-1196368	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:1195682-1196601	IMR90	lung:	n/a	n/a
6	MAZ	chr4:1195492-1196596	IMR90	lung:	n/a	n/a
7	POLR2A	chr4:1196185-1196375	HepG2	liver:	n/a	n/a
8	BHLHE40	chr4:1194261-1196355	GM12878	blood:	n/a	chr4:1195275-1195284 chr4:1195268-1195289
9	MAFK	chr4:1196189-1196395	Hela-S3	cervix:	n/a	chr4:1196239-1196254
10	MAFF	chr4:1195935-1196414	K562	blood:	n/a	chr4:1196238-1196256
11	TBP	chr4:1195176-1196265	GM12878	blood:	n/a	n/a
12	RUNX3	chr4:1195581-1196327	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:1194648-1196381	GM19193	blood:	n/a	n/a
14	RUNX3	chr4:1195559-1196285	GM12878	blood:	n/a	n/a
15	WRNIP1	chr4:1196232-1196321	GM12878	blood:	n/a	n/a
16	RAD21	chr4:1195696-1196363	IMR90	lung:	n/a	n/a
17	MAZ	chr4:1194684-1196461	GM12878	blood:	n/a	n/a
18	EP300	chr4:1195678-1196361	GM12878	blood:	n/a	n/a
19	CTCF	chr4:1196140-1196290	GM12873	blood:	n/a	n/a
20	MAX	chr4:1194217-1196329	NB4	blood:	n/a	n/a
21	EBF1	chr4:1195696-1196376	GM12878	blood:	n/a	n/a
22	MAFF	chr4:1196059-1196428	HepG2	liver:	n/a	chr4:1196238-1196256
23	MAX	chr4:1194291-1196300	GM12878	blood:	n/a	n/a
24	POLR2A	chr4:1195472-1196483	HL-60	blood:	n/a	n/a
25	MXI1	chr4:1195666-1196334	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:1195818-1196379	GM12878	blood:	n/a	n/a
27	POLR2A	chr4:1194623-1196275	GM12878	blood:	n/a	n/a
28	MAFK	chr4:1196158-1196356	H1-hESC	embryonic stem cell:	n/a	chr4:1196239-1196254
29	MAFK	chr4:1195676-1196681	IMR90	lung:	n/a	chr4:1195927-1195938 chr4:1196239-1196254
30	EP300	chr4:1195701-1196349	GM12878	blood:	n/a	n/a
31	POLR2A	chr4:1194604-1196246	GM15510	blood:	n/a	n/a
32	MAFK	chr4:1196060-1196427	HepG2	liver:	n/a	chr4:1196239-1196254
33	MXI1	chr4:1195511-1196582	IMR90	lung:	n/a	n/a
34	MAFK	chr4:1196056-1196430	HepG2	liver:	n/a	chr4:1196239-1196254
35	CHD2	chr4:1195681-1196395	GM12878	blood:	n/a	n/a
36	PAX5	chr4:1195582-1196315	GM12878	blood:	n/a	n/a
37	CEBPB	chr4:1195612-1196298	IMR90	lung:	n/a	chr4:1195807-1195818
38	POLR2A	chr4:1195598-1196462	HL-60	blood:	n/a	n/a
39	MTA3	chr4:1195539-1196294	GM12878	blood:	n/a	n/a
40	RFX5	chr4:1196184-1196256	HepG2	liver:	n/a	n/a
41	MAFK	chr4:1195985-1196433	K562	blood:	n/a	chr4:1196239-1196254

No.	Distal block	Cell Line	Cell type
1	chr4:1195937..1198894-chr4:1221468..1224458,3	K562	blood:
2	chr4:1196184..1198121-chr4:1199420..1202369,2	K562	blood:
3	chr4:1184981..1187238-chr4:1195672..1197196,2	MCF-7	breast:
4	chr4:1195791..1198447-chr4:1208482..1210775,2	MCF-7	breast:

Variant related genes	Relation type
SPON2	TF binding region
ENSG00000159674	Chromatin interaction
ENSG00000159692	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10011708	1.00[TSI][hapmap]
rs1250087	0.87[ASW][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes]
rs1272043	1.00[TSI][hapmap]
rs4974567	1.00[TSI][hapmap]
rs4974626	1.00[AMR][1000 genomes]
rs4974645	1.00[TSI][hapmap]
rs6836809	1.00[TSI][hapmap]
rs7659524	0.89[YRI][hapmap];0.85[AMR][1000 genomes]
rs7676912	1.00[TSI][hapmap]
rs900023	0.85[AMR][1000 genomes]
rs922697	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1009619	chr4:901897-1215657	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv1000381	chr4:927509-1198766	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
7	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
8	nsv878329	chr4:1147407-1254930	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
10	nsv593276	chr4:1159680-1227469	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv461151	chr4:1159680-1236840	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv593277	chr4:1159680-1236840	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv878331	chr4:1159680-1254930	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
14	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
15	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
16	nsv461153	chr4:1174861-1254930	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
17	nsv593279	chr4:1174861-1254930	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
18	nsv461154	chr4:1179213-1254930	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
19	nsv593280	chr4:1179213-1254930	Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
20	nsv878332	chr4:1179213-1254930	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
21	nsv997971	chr4:1191256-1518521	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
22	nsv878333	chr4:1193832-1254930	Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1185000-1204200	Enhancers	Fetal Muscle Leg	muscle
2	chr4:1187000-1197200	Weak transcription	HepG2	liver
3	chr4:1193200-1197600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:1193400-1197000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr4:1193400-1197200	Enhancers	Fetal Lung	lung
6	chr4:1193400-1197600	Enhancers	Primary hematopoietic stem cells	blood
7	chr4:1193600-1196600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:1193600-1197000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
9	chr4:1193600-1197400	Enhancers	Lung	lung
10	chr4:1193800-1196600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr4:1193800-1196800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr4:1194000-1196400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr4:1194200-1196600	Enhancers	HSMMtube	muscle
14	chr4:1194200-1196800	Flanking Active TSS	Dnd41	blood
15	chr4:1194200-1207800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:1194600-1196400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr4:1194600-1196600	Enhancers	Liver	Liver
18	chr4:1194600-1197400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:1194600-1201600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:1194600-1202400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:1194800-1197000	Weak transcription	Gastric	stomach
22	chr4:1194800-1197200	Enhancers	Muscle Satellite Cultured Cells	--
23	chr4:1194800-1199600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:1194800-1200400	Weak transcription	Ovary	ovary
25	chr4:1194800-1201400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:1194800-1201800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:1194800-1201800	Weak transcription	Osteobl	bone
28	chr4:1194800-1202000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:1194800-1203000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:1194800-1203400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr4:1195000-1196600	Enhancers	NH-A	brain
32	chr4:1195000-1196800	Bivalent Enhancer	Placenta	Placenta
33	chr4:1195000-1198000	Enhancers	Fetal Stomach	stomach
34	chr4:1195000-1201400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr4:1195000-1201600	Weak transcription	Right Atrium	heart
36	chr4:1195200-1196400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:1195200-1197600	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr4:1195200-1198200	Weak transcription	Stomach Mucosa	stomach
39	chr4:1195200-1198400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr4:1195200-1200000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:1195200-1200600	Weak transcription	Pancreas	Pancrea
42	chr4:1195200-1201200	Enhancers	Spleen	Spleen
43	chr4:1195200-1201400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:1195200-1201600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:1195200-1201600	Weak transcription	Right Ventricle	heart
46	chr4:1195200-1202600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:1195200-1204400	Weak transcription	HMEC	breast
48	chr4:1195200-1214600	Weak transcription	A549	lung
49	chr4:1195400-1196400	Enhancers	Colonic Mucosa	Colon
50	chr4:1195400-1196600	Enhancers	NHDF-Ad	bronchial

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