Variant report

Variant	rs6799210
Chromosome Location	chr3:196130005-196130006
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196129090..196131271-chr3:196133908..196136067,2	MCF-7	breast:
2	chr3:196124558..196126207-chr3:196129580..196132524,2	K562	blood:
3	chr3:196129528..196131514-chr3:196134157..196136154,2	K562	blood:
4	chr3:196115479..196118192-chr3:196129291..196130932,2	K562	blood:

Variant related genes	Relation type
ENSG00000241868	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11185525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11185536	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11185538	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11707862	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487829	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12638322	0.82[CHB][hapmap]
rs6770487	0.88[ASN][1000 genomes]
rs6770643	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers 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	98 gene(s)	inside rSNPs	diseases
2	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
4	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
5	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers 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	45 gene(s)	inside rSNPs	diseases
8	nsv1003764	chr3:196028141-196190687	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv536895	chr3:196028141-196190687	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	esv1844755	chr3:196057616-196190350	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
13	nsv878183	chr3:196072442-196181228	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
15	esv32642	chr3:196118819-196153861	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6799210	HES1	cis	cerebellum	SCAN
rs6799210	RNF168	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196073600-196135800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:196083600-196143800	Weak transcription	Psoas Muscle	Psoas
3	chr3:196084600-196131600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:196089600-196150000	Weak transcription	Small Intestine	intestine
5	chr3:196095600-196144400	Weak transcription	Fetal Heart	heart
6	chr3:196113200-196136400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:196115600-196134600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:196116200-196134000	Strong transcription	Fetal Intestine Small	intestine
9	chr3:196116600-196131800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:196116600-196133600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:196117800-196131600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:196118000-196133600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:196118000-196134800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:196118600-196157400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:196118800-196130400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:196118800-196133600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:196118800-196136000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:196120400-196130800	Strong transcription	GM12878-XiMat	blood
19	chr3:196120400-196133600	Weak transcription	Fetal Brain Male	brain
20	chr3:196121400-196134000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr3:196122400-196130200	Strong transcription	Fetal Intestine Large	intestine
22	chr3:196122400-196130600	Strong transcription	Fetal Thymus	thymus
23	chr3:196122400-196134200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:196123400-196134000	Strong transcription	Primary B cells from cord blood	blood
25	chr3:196123800-196130400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:196123800-196134600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:196124000-196130200	Strong transcription	Primary T cells from cord blood	blood
28	chr3:196124200-196134200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:196124400-196134200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:196124400-196134400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:196124600-196139600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:196124600-196147400	Weak transcription	Right Atrium	heart
33	chr3:196125000-196135400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:196125200-196133600	Weak transcription	Brain Substantia Nigra	brain
35	chr3:196125200-196157400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:196126600-196136000	Weak transcription	Colonic Mucosa	Colon
37	chr3:196127000-196133600	Weak transcription	HSMMtube	muscle
38	chr3:196127000-196133600	Weak transcription	NHLF	lung
39	chr3:196127000-196135400	Weak transcription	Fetal Kidney	kidney
40	chr3:196127000-196141200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:196127000-196141400	Weak transcription	HMEC	breast
42	chr3:196127000-196153800	Weak transcription	NHEK	skin
43	chr3:196127200-196131400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr3:196127200-196132000	Weak transcription	Osteobl	bone
45	chr3:196127200-196133600	Weak transcription	NH-A	brain
46	chr3:196127400-196133600	Weak transcription	NHDF-Ad	bronchial
47	chr3:196127400-196133800	Weak transcription	A549	lung
48	chr3:196127400-196141200	Weak transcription	Colon Smooth Muscle	Colon
49	chr3:196127400-196152600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:196127600-196131400	Weak transcription	H1 Cell Line	embryonic stem cell

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