Variant report

Variant	rs34229995
Chromosome Location	chr6:15244018-15244019
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr6:15243797-15248662	SK-N-SH	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:15226832..15230438-chr6:15243233..15244837,3	K562	blood:
2	chr6:15085986..15094450-chr6:15243173..15249347,32	MCF-7	breast:
3	chr6:15088518..15090840-chr6:15243708..15248817,8	MCF-7	breast:
4	chr6:15239185..15241876-chr6:15241948..15244748,3	MCF-7	breast:
5	chr6:15242226..15244729-chr6:15276839..15280020,3	K562	blood:
6	chr6:15147856..15151805-chr6:15244004..15248641,4	MCF-7	breast:
7	chr6:15087697..15092455-chr6:15243972..15249952,11	K562	blood:

No data

Variant related genes	Relation type
JARID2	TF binding region
ENSG00000264687	Chromatin interaction
ENSG00000234261	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs13191127	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13197919	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs13198600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13203059	1.00[AFR][1000 genomes]
rs13203659	1.00[AFR][1000 genomes]
rs13203744	1.00[AFR][1000 genomes]
rs13206138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13206695	0.85[EUR][1000 genomes]
rs13209122	0.92[EUR][1000 genomes]
rs13209721	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13210652	0.84[EUR][1000 genomes]
rs13213534	0.85[EUR][1000 genomes]
rs13215638	0.85[EUR][1000 genomes]
rs13216551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13216625	0.85[EUR][1000 genomes]
rs13219748	0.92[EUR][1000 genomes]
rs34048058	0.84[EUR][1000 genomes]
rs34144528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34156913	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34340185	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34390534	0.92[EUR][1000 genomes]
rs34470245	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34488826	1.00[EUR][1000 genomes]
rs34677259	0.92[EUR][1000 genomes]
rs34790337	0.84[EUR][1000 genomes]
rs34816087	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34816488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34934295	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35070076	1.00[AFR][1000 genomes]
rs35147300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35378362	0.92[EUR][1000 genomes]
rs35659244	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35660009	0.85[EUR][1000 genomes]
rs35981238	0.92[EUR][1000 genomes]
rs67845400	0.85[EUR][1000 genomes]
rs71533639	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71533640	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71533642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71551024	1.00[AFR][1000 genomes]
rs71551025	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs71551028	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71551030	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71551032	0.92[EUR][1000 genomes]
rs71551033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71551034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71551035	0.89[EUR][1000 genomes]
rs71551040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71551041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71551042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71551043	0.96[EUR][1000 genomes]
rs71551045	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs71551046	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7740407	0.92[EUR][1000 genomes]
rs9383028	0.85[EUR][1000 genomes]
rs9476760	0.85[EUR][1000 genomes]
rs9476761	0.85[EUR][1000 genomes]
rs9476782	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9476783	0.92[EUR][1000 genomes]
rs9476784	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9476790	1.00[AMR][1000 genomes]
rs9476793	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9476794	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9476797	0.92[EUR][1000 genomes]
rs9476798	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830593	chr6:15049636-15244190	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv830594	chr6:15171158-15261296	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS 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	29 gene(s)	inside rSNPs	diseases
5	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	28 gene(s)	inside rSNPs	diseases
7	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15240000-15244400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr6:15240000-15244600	Weak transcription	Left Ventricle	heart
3	chr6:15240000-15244600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:15240000-15244800	Weak transcription	Aorta	Aorta
5	chr6:15240000-15244800	Weak transcription	Right Atrium	heart
6	chr6:15240200-15244600	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:15240400-15244200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:15240400-15244200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:15240400-15244400	Weak transcription	Fetal Brain Female	brain
10	chr6:15240400-15244400	Weak transcription	Fetal Lung	lung
11	chr6:15240400-15244400	Weak transcription	Fetal Stomach	stomach
12	chr6:15240400-15244400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:15240400-15244600	Weak transcription	Brain Substantia Nigra	brain
14	chr6:15240400-15244600	Weak transcription	HSMMtube	muscle
15	chr6:15240600-15244400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:15240600-15244600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:15240600-15244600	Weak transcription	Brain Germinal Matrix	brain
18	chr6:15240600-15244600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:15240600-15244600	Weak transcription	HSMM	muscle
20	chr6:15240600-15244800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:15240800-15244200	Weak transcription	Fetal Heart	heart
22	chr6:15241000-15244600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:15242600-15244400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:15242800-15244200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr6:15242800-15244200	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr6:15242800-15244600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr6:15243000-15244200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:15243000-15244600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr6:15243000-15244600	Enhancers	HUVEC	blood vessel
30	chr6:15243000-15244800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr6:15243200-15244200	Enhancers	HepG2	liver
32	chr6:15243200-15244400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr6:15243200-15244400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr6:15243200-15244400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:15243200-15244600	Enhancers	Primary B cells from cord blood	blood
36	chr6:15243200-15245400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr6:15243200-15248400	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr6:15243400-15244200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:15243400-15244400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:15243400-15244400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr6:15243400-15244400	Enhancers	Primary hematopoietic stem cells	blood
42	chr6:15243400-15244400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:15243400-15244600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
44	chr6:15243400-15244600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:15243600-15244200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:15243600-15244600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:15243600-15244600	Enhancers	Adipose Nuclei	Adipose
48	chr6:15243600-15244600	Enhancers	Fetal Muscle Leg	muscle
49	chr6:15243600-15244600	Enhancers	Placenta	Placenta
50	chr6:15243600-15244600	Weak transcription	Placenta Amnion	Placenta Amnion

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