Variant report

Variant	rs3130660
Chromosome Location	chr6:30706361-30706362
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30706320-30707035	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:30706282-30707211	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr6:30704670-30712656	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr6:30705304-30707241	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr6:30706252-30707122	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:30704619-30712530	IMR90	lung:	n/a	n/a
7	NFYB	chr6:30706311-30706379	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:30706210-30706857	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:30706142-30706522	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr6:30705168-30707154	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr6:30704671-30707153	A549	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30706320-30706370	ECC-1	luminal epithelium:	n/a
2	chr6:30706320-30706370	HEK293	kidney:	embryo
3	chr6:30706320-30706370	GM12891	blood:	n/a
4	chr6:30706320-30706370	AG04450	lung:	fetal
5	chr6:30706320-30706370	AG09309	skin:	n/a
6	chr6:30706320-30706370	HRE	kidney:	n/a
7	chr6:30706320-30706370	IMR90	lung:	fetal
8	chr6:30706320-30706370	SK-N-SH	brain:	n/a
9	chr6:30706320-30706370	Caco-2	colon:	n/a
10	chr6:30706320-30706370	Hepatocyte	liver:	n/a
11	chr6:30706320-30706370	GM12892	blood:	n/a
12	chr6:30706320-30706370	AG10803	skin:	n/a
13	chr6:30706320-30706370	NHBE	bronchial:	n/a
14	chr6:30706320-30706370	HRPEpiC	eye:	n/a
15	chr6:30706320-30706370	U87	brain:	n/a
16	chr6:30706320-30706370	HMEC	breast:	n/a
17	chr6:30706320-30706370	PANC-1	pancreas:	n/a
18	chr6:30706320-30706370	HNPCEpiC	eye:	n/a
19	chr6:30706320-30706370	HCPEpiC	choroid plexus:	n/a
20	chr6:30706320-30706370	AoSMC	blood vessel:	n/a
21	chr6:30706320-30706370	BE2_C	brain:	n/a
22	chr6:30706320-30706370	HCT-116	colon:	n/a
23	chr6:30706320-30706370	HPAEpiC	pulmonary alveolar:	n/a
24	chr6:30706320-30706370	ovcar-3	ovarian:	n/a
25	chr6:30706320-30706370	HEEpiC	esophagus:	n/a
26	chr6:30706320-30706370	CMK	blood:	n/a
27	chr6:30706320-30706370	HRCEpiC	kidney:	n/a
28	chr6:30706320-30706370	SKMC	muscle:	n/a
29	chr6:30706320-30706370	GM06990	blood:	n/a
30	chr6:30706320-30706370	LNCaP	prostate:	n/a
31	chr6:30706320-30706370	GM12878	blood:	n/a
32	chr6:30706320-30706370	PFSK-1	brain:	n/a
33	chr6:30706320-30706370	HCF	heart:	n/a
34	chr6:30706320-30706370	HepG2	liver:	n/a
35	chr6:30706320-30706370	GM19239	blood:	n/a
36	chr6:30706320-30706370	SK-N-SH_RA	brain:	n/a
37	chr6:30706320-30706370	HUVEC	blood vessel:	n/a
38	chr6:30706320-30706370	K562	blood:	n/a
39	chr6:30706320-30706370	AG04449	skin:	fetal
40	chr6:30706320-30706370	HL-60	blood:	n/a
41	chr6:30706320-30706370	ProgFib	skin:	n/a
42	chr6:30706320-30706370	NB4	blood:	n/a
43	chr6:30706320-30706370	HCM	heart:	n/a
44	chr6:30706320-30706370	HIPEpiC	eye:	n/a
45	chr6:30706320-30706370	T-47D	breast:	n/a
46	chr6:30706320-30706370	RPTEC	kidney:	n/a
47	chr6:30706320-30706370	SAEC	small airway:	n/a
48	chr6:30706320-30706370	Hela-S3	cervix:	n/a
49	chr6:30706320-30706370	SK-N-MC	brain:	n/a
50	chr6:30706320-30706370	NHDF-neo	bronchial:	n/a

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122908445..122908984-chr6:30705769..30706382,2	Hela-S3	cervix:
2	chr6:30514949..30517776-chr6:30704916..30707043,2	K562	blood:
3	chr6:30581322..30587794-chr6:30705649..30714068,32	K562	blood:
4	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
5	chr6:30639079..30642784-chr6:30705636..30712325,12	MCF-7	breast:
6	chr6:30646395..30649153-chr6:30705465..30707695,2	MCF-7	breast:
7	chr6:30581143..30584983-chr6:30704116..30707481,6	MCF-7	breast:
8	chr6:30652832..30655180-chr6:30706103..30707894,2	MCF-7	breast:
9	chr6:30705562..30707889-chr6:31046785..31048860,2	K562	blood:
10	chr6:30705171..30717521-chr6:30843972..30856100,74	MCF-7	breast:
11	chr6:30704403..30722478-chr6:30842859..30858629,100	MCF-7	breast:
12	chr6:30591945..30594693-chr6:30703860..30706448,2	K562	blood:
13	chr6:30703055..30723531-chr6:30783853..30800217,151	MCF-7	breast:
14	chr6:30631685..30633412-chr6:30705703..30707816,2	MCF-7	breast:
15	chr6:30523433..30526056-chr6:30704817..30707811,2	K562	blood:
16	chr6:30592889..30594837-chr6:30705459..30708073,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000201988	TF binding region
ENSG00000272273	TF binding region
ENSG00000201988	CpG island
ENSG00000272273	CpG island
ENSG00000204576	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000137343	Chromatin interaction
ENSG00000146112	Chromatin interaction
ENSG00000214894	Chromatin interaction
ENSG00000222894	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1059612	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1264351	0.83[AMR][1000 genomes]
rs1264373	0.83[AMR][1000 genomes]
rs3094023	0.83[AMR][1000 genomes]
rs3094118	0.85[EUR][1000 genomes]
rs3094125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3095276	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3095326	0.87[EUR][1000 genomes]
rs3095327	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3095328	0.89[EUR][1000 genomes]
rs3095332	0.89[EUR][1000 genomes]
rs3095334	0.83[EUR][1000 genomes]
rs3129972	0.90[EUR][1000 genomes]
rs3129973	0.87[EUR][1000 genomes]
rs3129974	0.89[EUR][1000 genomes]
rs3129977	0.82[EUR][1000 genomes]
rs3129978	0.83[EUR][1000 genomes]
rs3129984	0.81[EUR][1000 genomes]
rs3130117	0.83[AMR][1000 genomes]
rs3130247	0.83[AMR][1000 genomes]
rs3130658	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3130665	0.85[EUR][1000 genomes]
rs3130668	0.81[EUR][1000 genomes]
rs3130673	0.83[EUR][1000 genomes]
rs3132582	0.92[EUR][1000 genomes]
rs3132583	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132599	0.83[EUR][1000 genomes]
rs3132600	0.87[EUR][1000 genomes]
rs3132603	0.83[EUR][1000 genomes]
rs3132605	0.83[EUR][1000 genomes]
rs9262126	0.95[EUR][1000 genomes]
rs9262130	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9262132	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9262135	0.95[EUR][1000 genomes]
rs9262141	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9262142	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9262143	0.92[EUR][1000 genomes]
rs9262146	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
6	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
8	nsv970736	chr6:30692055-30710740	Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
9	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong 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	179 gene(s)	inside rSNPs	diseases
10	nsv884101	chr6:30695920-30733121	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	163 gene(s)	inside rSNPs	diseases
11	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
12	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
13	nsv884102	chr6:30706013-30720567	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3130660	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30690000-30709600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:30690400-30709200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:30692600-30708200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:30693200-30708800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:30693400-30709000	Strong transcription	Fetal Stomach	stomach
6	chr6:30693800-30709000	Strong transcription	Fetal Brain Female	brain
7	chr6:30694000-30708800	Weak transcription	Fetal Brain Male	brain
8	chr6:30694400-30707800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:30695400-30708200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:30695400-30709000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:30695400-30709200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr6:30695600-30707800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:30696200-30707400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:30696400-30709000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:30696600-30706800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:30696800-30707400	Strong transcription	NHLF	lung
17	chr6:30697000-30707600	Strong transcription	Osteobl	bone
18	chr6:30697000-30707800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:30697000-30708600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:30697000-30709200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:30698800-30706600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:30698800-30707400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:30698800-30707800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:30698800-30708200	Strong transcription	Liver	Liver
25	chr6:30698800-30708200	Strong transcription	Brain Hippocampus Middle	brain
26	chr6:30698800-30708200	Strong transcription	Fetal Intestine Small	intestine
27	chr6:30698800-30708600	Strong transcription	Brain Anterior Caudate	brain
28	chr6:30698800-30709000	Strong transcription	Fetal Intestine Large	intestine
29	chr6:30698800-30709200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:30699200-30707800	Strong transcription	Stomach Smooth Muscle	stomach
31	chr6:30700000-30707600	Strong transcription	Ovary	ovary
32	chr6:30700600-30709200	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr6:30700800-30706800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:30701200-30708400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:30701600-30706600	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr6:30702000-30707800	Strong transcription	Rectal Smooth Muscle	rectum
37	chr6:30702200-30708600	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr6:30702400-30706400	Enhancers	Primary B cells from cord blood	blood
39	chr6:30702400-30708600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:30702400-30709200	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr6:30702600-30708800	Strong transcription	Brain Germinal Matrix	brain
42	chr6:30703000-30706400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:30703200-30706600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:30703400-30707400	Strong transcription	NHDF-Ad	bronchial
45	chr6:30703400-30709200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:30703600-30709000	Genic enhancers	Adipose Nuclei	Adipose
47	chr6:30703800-30706400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr6:30704200-30708000	Strong transcription	Brain Cingulate Gyrus	brain
49	chr6:30704400-30706600	Genic enhancers	Rectal Mucosa Donor 31	rectum
50	chr6:30704600-30706800	Genic enhancers	Spleen	Spleen

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