Variant report

Variant	rs34856311
Chromosome Location	chr19:40031369-40031370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:61)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:40031360-40031510	BJ	skin:	n/a	n/a
2	BCL3	chr19:40029763-40031451	A549	lung:	n/a	chr19:40031264-40031273
3	ATF3	chr19:40030522-40031481	A549	lung:	n/a	n/a
4	CTCF	chr19:40029208-40032099	A549	lung:	n/a	n/a
5	HCFC1	chr19:40029642-40031379	Hela-S3	cervix:	n/a	n/a
6	NRF1	chr19:40029898-40031447	SK-N-SH	brain:	n/a	chr19:40030798-40030809 chr19:40030796-40030810 chr19:40030886-40030900 chr19:40030907-40030916 chr19:40030889-40030900 chr19:40030889-40030903 chr19:40030889-40030898 chr19:40030799-40030810
7	REST	chr19:40030459-40031507	A549	lung:	n/a	chr19:40031264-40031273
8	MAZ	chr19:40029624-40031486	IMR90	lung:	n/a	n/a
9	REST	chr19:40029734-40031483	H1-neurons	neurons:	n/a	chr19:40031264-40031273
10	CTCF	chr19:40031300-40031450	HCM	heart:	n/a	n/a
11	EGR1	chr19:40030508-40031409	HCT-116	colon:	n/a	chr19:40030803-40030816 chr19:40030805-40030815 chr19:40030890-40030899 chr19:40030803-40030817 chr19:40030800-40030809 chr19:40030799-40030821 chr19:40030804-40030815 chr19:40030801-40030810 chr19:40030805-40030814 chr19:40030803-40030816 chr19:40030803-40030816
12	CTCF	chr19:40031260-40031410	BJ	skin:	n/a	n/a
13	CTCF	chr19:40031260-40031410	HPAF	blood vessel:	n/a	n/a
14	CTCF	chr19:40031220-40031370	HVMF	connective:	n/a	n/a
15	REST	chr19:40029988-40031371	PANC-1	pancreas:	n/a	chr19:40031264-40031273
16	SIN3AK20	chr19:40030531-40031393	A549	lung:	n/a	n/a
17	SIN3AK20	chr19:40029040-40031544	PANC-1	pancreas:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:40031368-40031418	HMEC	breast:	n/a
2	chr19:40031368-40031418	HUVEC	blood vessel:	n/a
3	chr19:40031368-40031418	Hela-S3	cervix:	n/a
4	chr19:40031368-40031418	CMK	blood:	n/a
5	chr19:40031368-40031418	SKMC	muscle:	n/a
6	chr19:40031368-40031418	NH-A	brain:	n/a
7	chr19:40031368-40031418	GM12892	blood:	n/a
8	chr19:40031368-40031418	SAEC	small airway:	n/a
9	chr19:40031368-40031418	AG04450	lung:	fetal
10	chr19:40031368-40031418	AG10803	skin:	n/a
11	chr19:40031368-40031418	ECC-1	luminal epithelium:	n/a
12	chr19:40031368-40031418	GM06990	blood:	n/a
13	chr19:40031368-40031418	LNCaP	prostate:	n/a
14	chr19:40031368-40031418	GM12891	blood:	n/a
15	chr19:40031368-40031418	PANC-1	pancreas:	n/a
16	chr19:40031368-40031418	HCM	heart:	n/a
17	chr19:40031368-40031418	NHDF-neo	bronchial:	n/a
18	chr19:40031368-40031418	GM19239	blood:	n/a
19	chr19:40031368-40031418	MCF10A-Er-Src	breast:	n/a
20	chr19:40031368-40031418	HPAEpiC	pulmonary alveolar:	n/a
21	chr19:40031368-40031418	HepG2	liver:	n/a
22	chr19:40031368-40031418	SK-N-MC	brain:	n/a
23	chr19:40031368-40031418	ovcar-3	ovarian:	n/a
24	chr19:40031368-40031418	NHBE	bronchial:	n/a
25	chr19:40031368-40031418	K562	blood:	n/a
26	chr19:40031368-40031418	HL-60	blood:	n/a
27	chr19:40031368-40031418	BJ	skin:	n/a
28	chr19:40031368-40031418	HAEpiC	amniotic membrane:	n/a
29	chr19:40031368-40031418	AG09309	skin:	n/a
30	chr19:40031368-40031418	SK-N-SH_RA	brain:	n/a
31	chr19:40031368-40031418	H1-hESC	embryonic stem cell:	embryo
32	chr19:40031368-40031418	HNPCEpiC	eye:	n/a
33	chr19:40031368-40031418	HCF	heart:	n/a
34	chr19:40031368-40031418	ProgFib	skin:	n/a
35	chr19:40031368-40031418	AG04449	skin:	fetal
36	chr19:40031368-40031418	HEK293	kidney:	embryo
37	chr19:40031368-40031418	HIPEpiC	eye:	n/a
38	chr19:40031368-40031418	Jurkat	blood:	n/a
39	chr19:40031368-40031418	AG09319	gingival:	n/a
40	chr19:40031368-40031418	HEEpiC	esophagus:	n/a
41	chr19:40031368-40031418	T-47D	breast:	n/a
42	chr19:40031368-40031418	IMR90	lung:	fetal
43	chr19:40031368-40031418	NB4	blood:	n/a
44	chr19:40031368-40031418	MCF-7	breast:	n/a
45	chr19:40031368-40031418	RPTEC	kidney:	n/a
46	chr19:40031368-40031418	GM12878	blood:	n/a
47	chr19:40031368-40031418	HCT-116	colon:	n/a
48	chr19:40031368-40031418	PFSK-1	brain:	n/a
49	chr19:40031368-40031418	HRE	kidney:	n/a
50	chr19:40031368-40031418	BE2_C	brain:	n/a

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40029767..40032366-chr19:40330875..40333585,2	K562	blood:
2	chr19:39891586..39893179-chr19:40030915..40033387,2	MCF-7	breast:
3	chr19:40031156..40032719-chr19:40323225..40324981,2	MCF-7	breast:
4	chr19:39933642..39937454-chr19:40029470..40032868,6	MCF-7	breast:
5	chr19:39934417..39936200-chr19:40029570..40032204,2	MCF-7	breast:
6	chr19:39901022..39904778-chr19:40029097..40032980,4	MCF-7	breast:
7	chr19:39959218..39961854-chr19:40028748..40031663,2	K562	blood:
8	chr19:39924990..39926577-chr19:40031100..40033171,2	MCF-7	breast:
9	chr19:40023614..40026391-chr19:40028689..40031990,5	MCF-7	breast:
10	chr19:40019907..40024445-chr19:40029285..40031709,4	MCF-7	breast:
11	chr19:39931001..39933171-chr19:40029480..40031756,2	MCF-7	breast:
12	chr19:39925003..39927867-chr19:40028857..40032200,4	K562	blood:
13	chr19:39923771..39928393-chr19:40029138..40032183,4	MCF-7	breast:

No data

Variant related genes	Relation type
EID2	TF binding region
EID2	CpG island
ENSG00000105193	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000105204	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000105202	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000269584	Chromatin interaction
ENSG00000176401	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12608773	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12609985	0.95[CEU][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap]
rs12610740	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12610751	0.95[CEU][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.80[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12610833	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12611125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12972285	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12972675	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12973775	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12978311	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12980249	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1368469	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17641650	0.95[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes]
rs17795475	0.87[ASW][hapmap];0.95[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1836011	0.95[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap]
rs34126123	0.84[EUR][1000 genomes]
rs34271968	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34355544	0.83[EUR][1000 genomes]
rs34885802	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35038530	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35939822	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3746086	0.91[ASN][1000 genomes]
rs4803258	0.87[ASW][hapmap];0.90[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4803259	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55994613	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59485553	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60587381	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67832846	0.84[EUR][1000 genomes]
rs7247184	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7247218	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7257553	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7257904	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7258348	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7507648	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription 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	31 gene(s)	inside rSNPs	diseases
4	nsv911693	chr19:39986241-40033574	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv579509	chr19:40004640-40133438	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv911694	chr19:40015907-40031369	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs34856311	SNRPD2	cis	cerebellum	SCAN
rs34856311	EID2B	cis	lymphoblastoid	seeQTL
rs34856311	DHX34	cis	cerebellum	SCAN
rs34856311	GSK3A	cis	cerebellum	SCAN
rs34856311	MRPS12	cis	lymphoblastoid	seeQTL
rs34856311	CBLC	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40029200-40031400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr19:40030000-40031400	Active TSS	Brain Germinal Matrix	brain
3	chr19:40030000-40031400	Active TSS	Fetal Brain Male	brain
4	chr19:40030200-40031400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr19:40030200-40031400	Active TSS	Stomach Smooth Muscle	stomach
6	chr19:40030200-40031400	Active TSS	NH-A	brain
7	chr19:40030800-40031600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:40030800-40031600	Enhancers	Colon Smooth Muscle	Colon
9	chr19:40030800-40033000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr19:40031000-40031400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr19:40031000-40031400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:40031000-40031400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:40031000-40031400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr19:40031000-40031400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr19:40031000-40031400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:40031000-40031400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:40031000-40031400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr19:40031000-40031400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr19:40031000-40031400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:40031000-40031400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr19:40031000-40031400	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr19:40031000-40031400	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr19:40031000-40031400	Flanking Active TSS	Fetal Brain Female	brain
24	chr19:40031000-40031400	Enhancers	Fetal Stomach	stomach
25	chr19:40031000-40031400	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr19:40031000-40031400	Flanking Bivalent TSS/Enh	HepG2	liver
27	chr19:40031000-40031400	Flanking Active TSS	HUVEC	blood vessel
28	chr19:40031000-40031400	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr19:40031000-40031600	Flanking Active TSS	A549	lung
30	chr19:40031000-40031600	Flanking Active TSS	K562	blood
31	chr19:40031000-40031800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr19:40031000-40032800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:40031000-40037200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:40031200-40031400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:40031200-40031400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr19:40031200-40031400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr19:40031200-40031400	Enhancers	Primary B cells from cord blood	blood
38	chr19:40031200-40031400	Enhancers	Primary B cells from peripheral blood	blood
39	chr19:40031200-40031400	Enhancers	Primary T cells from cord blood	blood
40	chr19:40031200-40031400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr19:40031200-40031400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:40031200-40031400	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr19:40031200-40031400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr19:40031200-40031400	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr19:40031200-40031400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:40031200-40031400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:40031200-40031400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr19:40031200-40031400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:40031200-40031400	Enhancers	Adipose Nuclei	Adipose
50	chr19:40031200-40031400	Flanking Active TSS	Brain Angular Gyrus	brain

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