Variant report

Variant	rs34677724
Chromosome Location	chr19:18967721-18967722
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	RAD21	chr19:18967115-18967795	SK-N-SH	brain:	n/a	chr19:18967620-18967633
2	POLR2A	chr19:18965802-18967757	GM12892	blood:	n/a	n/a
3	POLR2A	chr19:18967549-18968004	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:18967512-18967751	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr19:18967338-18967747	K562	blood:	n/a	n/a
6	POLR2A	chr19:18967244-18967786	K562	blood:	n/a	n/a
7	POLR2A	chr19:18967224-18967763	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr19:18963957-18968889	K562	blood:	n/a	n/a
9	SMC3	chr19:18966860-18967745	SK-N-SH	brain:	n/a	chr19:18967635-18967642 chr19:18967116-18967126
10	POLR2A	chr19:18967565-18967885	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:18966583-18968631	GM12892	blood:	n/a	n/a
12	POLR2A	chr19:18963959-18968495	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:18967533-18967798	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:18966531..18969401-chr19:18973021..18975887,3	MCF-7	breast:

Variant related genes	Relation type
UPF1	TF binding region
ENSG00000005007	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10412694	1.00[EUR][1000 genomes]
rs10416469	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416612	1.00[ASW][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10421797	1.00[CHD][hapmap]
rs55824320	1.00[EUR][1000 genomes]
rs56165767	0.89[EUR][1000 genomes]
rs56368502	1.00[EUR][1000 genomes]
rs58841981	0.83[EUR][1000 genomes]
rs61077411	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911293	chr19:18872917-19050957	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases
2	nsv911294	chr19:18872917-19093619	Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv833777	chr19:18875936-19031076	Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv911297	chr19:18928480-19077385	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911298	chr19:18928480-19093619	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv911299	chr19:18939954-18984843	Active TSS Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv911300	chr19:18944025-19093619	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv470132	chr19:18964442-19054720	Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18951800-18977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:18953200-18977600	Weak transcription	Fetal Heart	heart
3	chr19:18954800-18979800	Strong transcription	Dnd41	blood
4	chr19:18956200-18978400	Strong transcription	Thymus	Thymus
5	chr19:18956600-18972000	Genic enhancers	Fetal Muscle Trunk	muscle
6	chr19:18956800-18975200	Strong transcription	HepG2	liver
7	chr19:18958200-18977000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr19:18958400-18977600	Strong transcription	Fetal Intestine Large	intestine
9	chr19:18958400-18979000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr19:18958400-18979200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr19:18958400-18979400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr19:18958400-18979400	Strong transcription	Primary T cells from cord blood	blood
13	chr19:18958400-18979400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr19:18958400-18980200	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr19:18958600-18973200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
16	chr19:18958600-18976200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:18958600-18979000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:18958600-18979200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr19:18958600-18979400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr19:18958600-18979600	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr19:18958800-18979200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr19:18958800-18979200	Strong transcription	Brain Germinal Matrix	brain
23	chr19:18959000-18979000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr19:18959000-18979000	Strong transcription	Gastric	stomach
25	chr19:18959200-18979200	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr19:18959800-18978800	Strong transcription	Fetal Brain Female	brain
27	chr19:18960000-18979400	Strong transcription	Placenta Amnion	Placenta Amnion
28	chr19:18960400-18977600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:18960400-18978600	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:18960400-18978800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:18960400-18979200	Strong transcription	Fetal Intestine Small	intestine
32	chr19:18960600-18968400	Weak transcription	Psoas Muscle	Psoas
33	chr19:18960600-18977000	Strong transcription	Primary hematopoietic stem cells	blood
34	chr19:18960600-18979000	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr19:18960600-18979200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:18960600-18979400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr19:18960600-18979600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr19:18960600-18982600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:18960800-18973600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
40	chr19:18960800-18974800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr19:18960800-18975400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr19:18960800-18979200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:18960800-18979400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:18960800-18979400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:18961000-18972400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr19:18961000-18979200	Strong transcription	Osteobl	bone
47	chr19:18961000-18979400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr19:18961000-18979600	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr19:18961000-18979600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:18961200-18970400	Strong transcription	Primary T killer memory cells from peripheral blood	blood

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